UBE2T
ubiquitin conjugating enzyme E2 T, the group of FA complementation groups|Ubiquitin conjugating enzymes E2
Basic information
Region (hg38): 1:202331544-202341984
Links
Phenotypes
GenCC
Source:
- Fanconi anemia complementation group T (Strong), mode of inheritance: AR
- Fanconi anemia (Supportive), mode of inheritance: AR
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Fanconi anemia, complementation group T | AR | Cardiovascular; Hematologic; Oncologic | In Fanconi anemia, specific treatments can help manifestations (eg, oral androgens for blood counts; G-CSF for neutrophil count); HSCT can be curative, but solid tumor risk may remain; Surveillance for complications such as bone marrow failure is recommended; Fanconi anemia can involve congenital cardiac (and other) anomalies, and awareness may allow early management | Cardiovascular; Hematologic; Musculoskeletal; Neurologic; Oncologic | 20301575; 26046368 |
ClinVar
This is a list of variants' phenotypes submitted to
- not provided (1 variants)
- Fanconi anemia complementation group T (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the UBE2T gene is commonly pathogenic or not.
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.
| Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
|---|---|---|---|---|---|---|
| synonymous | 6 | |||||
| missense | 10 | 11 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 1 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 2 | |||||
| splice region | 1 | 1 | 2 | |||
| non coding | 12 | |||||
| Total | 2 | 2 | 11 | 12 | 5 |
Highest pathogenic variant AF is 0.00000658
Variants in UBE2T
This is a list of pathogenic ClinVar variants found in the UBE2T region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| UBE2T | protein_coding | protein_coding | ENST00000367274 | 6 | 10324 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0000106 | 0.587 | 125715 | 0 | 31 | 125746 | 0.000123 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.316 | 96 | 105 | 0.913 | 0.00000495 | 1292 |
| Missense in Polyphen | 39 | 46.792 | 0.83348 | 562 | ||
| Synonymous | 0.486 | 32 | 35.7 | 0.897 | 0.00000168 | 366 |
| Loss of Function | 0.809 | 9 | 12.0 | 0.748 | 8.44e-7 | 115 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000393 | 0.000391 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000652 | 0.000653 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000623 | 0.0000615 |
| Middle Eastern | 0.000652 | 0.000653 |
| South Asian | 0.0000653 | 0.0000653 |
| Other | 0.000163 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: Accepts ubiquitin from the E1 complex and catalyzes its covalent attachment to other proteins. Catalyzes monoubiquitination. Involved in mitomycin-C (MMC)-induced DNA repair. Acts as a specific E2 ubiquitin-conjugating enzyme for the Fanconi anemia complex by associating with E3 ubiquitin-protein ligase FANCL and catalyzing monoubiquitination of FANCD2, a key step in the DNA damage pathway (PubMed:16916645, PubMed:17938197, PubMed:19111657, PubMed:19589784, PubMed:28437106). Also mediates monoubiquitination of FANCL and FANCI (PubMed:16916645, PubMed:17938197, PubMed:19111657, PubMed:19589784). May contribute to ubiquitination and degradation of BRCA1 (PubMed:19887602). In vitro able to promote polyubiquitination using all 7 ubiquitin Lys residues, but may prefer 'Lys-11'-, 'Lys-27'-, 'Lys-48'- and 'Lys- 63'-linked polyubiquitination (PubMed:20061386). {ECO:0000269|PubMed:16916645, ECO:0000269|PubMed:17938197, ECO:0000269|PubMed:19111657, ECO:0000269|PubMed:19589784, ECO:0000269|PubMed:19887602, ECO:0000269|PubMed:20061386, ECO:0000269|PubMed:28437106}.;
- Disease
- DISEASE: Fanconi anemia complementation group T (FANCT) [MIM:616435]: A disorder affecting all bone marrow elements and resulting in anemia, leukopenia and thrombopenia. It is associated with cardiac, renal and limb malformations, dermal pigmentary changes, and a predisposition to the development of malignancies. At the cellular level it is associated with hypersensitivity to DNA-damaging agents, chromosomal instability (increased chromosome breakage) and defective DNA repair. {ECO:0000269|PubMed:26046368}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
- Pathway
- Fanconi anemia pathway - Homo sapiens (human);Gastric Cancer Network 2;Fanconi Anemia Pathway;DNA Repair;Post-translational protein modification;protein ubiquitylation;Metabolism of proteins;Synthesis of active ubiquitin: roles of E1 and E2 enzymes;Fanconi anemia pathway;Protein ubiquitination
(Consensus)
Recessive Scores
- pRec
- 0.0486
Intolerance Scores
- loftool
- 0.774
- rvis_EVS
- -0.12
- rvis_percentile_EVS
- 44.54
Haploinsufficiency Scores
- pHI
- 0.155
- hipred
- Y
- hipred_score
- 0.579
- ghis
- 0.602
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.621
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Ube2t
- Phenotype
Gene ontology
- Biological process
- DNA repair;protein monoubiquitination;cellular response to DNA damage stimulus;protein ubiquitination;protein K29-linked ubiquitination;interstrand cross-link repair;protein K27-linked ubiquitination;protein autoubiquitination;protein K63-linked ubiquitination;protein K48-linked ubiquitination;protein K11-linked ubiquitination;protein K6-linked ubiquitination
- Cellular component
- nucleus;nucleoplasm;nucleolus
- Molecular function
- chromatin binding;ubiquitin-protein transferase activity;protein binding;ATP binding;ubiquitin protein ligase binding;ubiquitin conjugating enzyme activity