EEF1B2

protein-coding

eukaryotic translation elongation factor 1 beta 2, the group of Small nucleolar RNA protein coding host genes

Gene summary

This gene encodes a translation elongation factor. The protein is a guanine nucleotide exchange factor involved in the transfer of aminoacylated tRNAs to the ribosome. Alternative splicing results in three transcript variants which differ only in the 5' UTR. [provided by RefSeq, Jul 2008]

MANE transcript

NM_001959.4

Inheritance

ClinVar variants

P:4U:30B:6

Top phenotype

neurodevelopmental disorder

gnomAD constraint

pLI —, LoF o/e 0.33

Max pathogenic AF

—

Genomic locus

chr2:206,159,585-206,162,928

External References & Databases

Ensembl (ENSG00000114942)

Transcript & Mutation Effects

hg38 • Region Span ~3.3 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

neurodevelopmental disorderLIMITED

Inheritance Pattern: AR

Disease ID:MONDO:0700092

Submitter: G2P

neurodevelopmental disorderSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0700092

Submitter: PanelApp Australia

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to EEF1B2 variants in ClinVar

8 Conditions Cataloged

Inborn genetic diseasesTotal: 25

not providedTotal: 5

not specifiedTotal: 4

Global developmental delayTotal: 2

Moderate global developmental delayTotal: 1

EEF1B2-related conditionTotal: 1

SeizureTotal: 1

Intellectual disabilityTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001959.4. 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				5 clinvar		5
missense			29 clinvar	1 clinvar		30
nonsense	2 clinvar					2
start loss						0
frameshift	1 clinvar					1
splice donor/acceptor (+/-2bp)	1 clinvar		1 clinvar			2
Total	4	0	30	6	0	40

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 76 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001959.4	RefSeq	NP_001950.1	6	MANE Select
ENST00000392222.7	Ensembl	ENSP00000376056.2	6	MANE Select
NM_001037663.2	RefSeq	NP_001032752.1	6	Standard
NM_021121.4	RefSeq	NP_066944.1	6	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Translation Factors
Translation
Metabolism of proteins
Eukaryotic Translation Elongation

Biological Process

translational elongation
response to ethanol

Molecular Function

translation elongation factor activity
protein binding

Cellular Component

nucleus
cytoplasm
endoplasmic reticulum
cytosol
eukaryotic translation elongation factor 1 complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000392222
Coding exons: 6
Length: 3344
Individuals with no LoFs: 125739
Homozygous LoFs: 0
Heterozygous LoFs: 9
Defined: 125748
p: 0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.327	114	124	0.917	0.00000606	1474
Missense (PolyPhen)		14	20.186	0.69354		278
Synonymous	-0.347	51	47.9	1.06	0.00000266	414
Loss of Function	2.17	4	12.2	0.329	5.12e-7	154

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000058	0.000058	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00011	0.00011	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.000018	0.000018	rare
South Asian	0.000033	0.000033	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: EF-1-beta and EF-1-delta stimulate the exchange of GDP bound to EF-1-alpha to GTP.;

Recessive Scores

pRec: 0.277

Intolerance Scores

LoFtool: 0.367
RVIS EVS: -0.03
RVIS percentile EVS: 51.4

Essentials

Essential (CRISPR): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.995

Gene Damage Prediction

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