EFTUD2
Basic information
Region (hg38): 17:44849948-44899445
Links
Phenotypes
GenCC
Source:
- 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:
Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
---|---|---|---|---|---|
Mandibulofacial dysostosis, Guion-Almeida type | AD | Audiologic/Otolaryngologic; Cardiovascular | Though 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 management | Audiologic/Otolaryngologic; Cardiovascular; Craniofacial; Gastrointestinal; Musculoskeletal; Neurologic | 16760738; 19334086; 22541558; 22305528; 23188108; 25790162 |
ClinVar
This is a list of variants' phenotypes submitted to
- 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.
Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
---|---|---|---|---|---|---|
synonymous | 113 | 132 | ||||
missense | 19 | 217 | 28 | 274 | ||
nonsense | 18 | 26 | ||||
start loss | 1 | 1 | ||||
frameshift | 41 | 23 | 64 | |||
splice donor/acceptor (+/-2bp) | 22 | 19 | 42 | |||
Total | 90 | 70 | 226 | 141 | 12 |
Highest pathogenic variant AF is 0.00000657004
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
EFTUD2 | protein_coding | protein_coding | ENST00000426333 | 27 | 49720 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
1.00 | 6.08e-8 | 125713 | 0 | 1 | 125714 | 0.00000398 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 4.03 | 293 | 561 | 0.522 | 0.0000314 | 6417 |
Missense in Polyphen | 75 | 243.93 | 0.30746 | 2766 | ||
Synonymous | 0.545 | 212 | 222 | 0.954 | 0.0000135 | 1870 |
Loss of Function | 6.45 | 1 | 50.4 | 0.0198 | 0.00000247 | 610 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.00 | 0.00 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.00 | 0.00 |
Finnish | 0.0000462 | 0.0000462 |
European (Non-Finnish) | 0.00 | 0.00 |
Middle Eastern | 0.00 | 0.00 |
South Asian | 0.00 | 0.00 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- 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
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
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