EFTUD2

elongation factor Tu GTP binding domain containing 2, the group of Spliceosomal C complex|U5 small nuclear ribonucleoprotein|Spliceosomal Bact complex|Spliceosomal P complex

Basic information

Region (hg38): 17:44849948-44899445

Links

ENSG00000108883NCBI:9343OMIM:603892HGNC:30858Uniprot:Q15029AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

  • mandibulofacial dysostosis-microcephaly syndrome (Definitive), mode of inheritance: AD
  • mandibulofacial dysostosis-microcephaly syndrome (Strong), mode of inheritance: AD
  • mandibulofacial dysostosis-microcephaly syndrome (Supportive), mode of inheritance: AD
  • mandibulofacial dysostosis-microcephaly syndrome (Definitive), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Mandibulofacial dysostosis, Guion-Almeida typeADAudiologic/Otolaryngologic; CardiovascularThough the condition may be recognizable, early recognition and treatment of hearing impairment may improve outcomes, including speech and language development; Recognition of potential GI manifestations (eg, Hirschsprung disease) may allow prompt treatment; The condition can involve congenital cardiac anomalies, and awareness may allow early managementAudiologic/Otolaryngologic; Cardiovascular; Craniofacial; Gastrointestinal; Musculoskeletal; Neurologic16760738; 19334086; 22541558; 22305528; 23188108; 25790162

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the EFTUD2 gene.

  • not_provided (577 variants)
  • Mandibulofacial_dysostosis-microcephaly_syndrome (118 variants)
  • Inborn_genetic_diseases (69 variants)
  • EFTUD2-related_disorder (29 variants)
  • not_specified (24 variants)
  • See_cases (4 variants)
  • Global_developmental_delay (2 variants)
  • Neurodevelopmental_disorder (1 variants)
  • Cleft_lip/palate (1 variants)
  • Hereditary_syndromic_Pierre_Robin_syndrome (1 variants)
  • Esophageal_atresia/tracheoesophageal_fistula (1 variants)
  • Chromatinopathy (1 variants)
  • Congenital_anomaly_of_kidney_and_urinary_tract (1 variants)
  • Mandibulofacial_dysostosis (1 variants)
  • Seizure (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EFTUD2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000004247.4. 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.

EffectPLPVUSLBBSum
synonymous
1
clinvar
1
clinvar
8
clinvar
113
clinvar
9
clinvar
132
missense
7
clinvar
19
clinvar
217
clinvar
28
clinvar
3
clinvar
274
nonsense
18
clinvar
8
clinvar
26
start loss
1
1
frameshift
41
clinvar
23
clinvar
64
splice donor/acceptor (+/-2bp)
22
clinvar
19
clinvar
1
clinvar
42
Total 90 70 226 141 12

Highest pathogenic variant AF is 0.00000657004

Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
EFTUD2protein_codingprotein_codingENST00000426333 2749720
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
1.006.08e-8125713011257140.00000398
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense4.032935610.5220.00003146417
Missense in Polyphen75243.930.307462766
Synonymous0.5452122220.9540.00001351870
Loss of Function6.45150.40.01980.00000247610

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.000.00
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.00004620.0000462
European (Non-Finnish)0.000.00
Middle Eastern0.000.00
South Asian0.000.00
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: Component of the U5 snRNP and the U4/U6-U5 tri-snRNP complex required for pre-mRNA splicing. Binds GTP.;
Disease
DISEASE: Mandibulofacial dysostosis with microcephaly (MFDM) [MIM:610536]: A rare syndrome characterized by progressive microcephaly, midface and malar hypoplasia, micrognathia, microtia, dysplastic ears, preauricular skin tags, significant developmental delay, and speech delay. Many patients have major sequelae, including choanal atresia that results in respiratory difficulties, conductive hearing loss, and cleft palate. {ECO:0000269|PubMed:22305528}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Pathway
Spliceosome - Homo sapiens (human);mRNA Processing;Metabolism of RNA;mRNA Splicing - Major Pathway;mRNA Splicing - Minor Pathway;mRNA Splicing;Processing of Capped Intron-Containing Pre-mRNA (Consensus)

Recessive Scores

pRec
0.337

Intolerance Scores

loftool
0.0218
rvis_EVS
-1.15
rvis_percentile_EVS
6.23

Haploinsufficiency Scores

pHI
0.237
hipred
Y
hipred_score
0.717
ghis
0.659

Essentials

essential_gene_CRISPR
E
essential_gene_CRISPR2
E
essential_gene_gene_trap
E
gene_indispensability_pred
E
gene_indispensability_score
0.989

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Eftud2
Phenotype
homeostasis/metabolism phenotype; immune system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); 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);

Zebrafish Information Network

Gene name
eftud2
Affected structure
neuroblast (sensu Vertebrata)
Phenotype tag
abnormal
Phenotype quality
increased occurrence

Gene ontology

Biological process
mRNA splicing, via spliceosome;mRNA processing;RNA splicing;cellular response to drug;response to cocaine
Cellular component
nucleoplasm;spliceosomal complex;cytosol;Cajal body;membrane;nuclear speck;U4/U6 x U5 tri-snRNP complex;U2-type catalytic step 2 spliceosome;catalytic step 2 spliceosome;ribonucleoprotein complex
Molecular function
RNA binding;GTPase activity;protein binding;GTP binding;U5 snRNA binding