UBE2D1
ubiquitin conjugating enzyme E2 D1, the group of Ubiquitin conjugating enzymes E2
Basic information
Region (hg38): 10:58334979-58370751
Previous symbols: [ "SFT" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the UBE2D1 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 | 0 | |||||
| missense | 1 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 1 | 0 | 0 |
Variants in UBE2D1
This is a list of pathogenic ClinVar variants found in the UBE2D1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 10-58361356-C-T | not specified | Uncertain significance (Jul 25, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| UBE2D1 | protein_coding | protein_coding | ENST00000373910 | 7 | 35779 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.120 | 0.857 | 125634 | 0 | 5 | 125639 | 0.0000199 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.03 | 27 | 77.2 | 0.350 | 0.00000373 | 955 |
| Missense in Polyphen | 17 | 36.911 | 0.46057 | 474 | ||
| Synonymous | 0.222 | 25 | 26.5 | 0.945 | 0.00000143 | 262 |
| Loss of Function | 1.96 | 3 | 9.52 | 0.315 | 4.00e-7 | 126 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000545 | 0.0000544 |
| Finnish | 0.0000468 | 0.0000462 |
| European (Non-Finnish) | 0.0000268 | 0.0000264 |
| Middle Eastern | 0.0000545 | 0.0000544 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Accepts ubiquitin from the E1 complex and catalyzes its covalent attachment to other proteins (PubMed:22496338). In vitro catalyzes 'Lys-48'-linked polyubiquitination (PubMed:20061386). Mediates the selective degradation of short-lived and abnormal proteins. Functions in the E6/E6-AP-induced ubiquitination of p53/TP53. Mediates ubiquitination of PEX5 and auto-ubiquitination of STUB1, TRAF6 and TRIM63/MURF1 (PubMed:18042044, PubMed:18359941). Ubiquitinates STUB1-associated HSP90AB1 in vitro (PubMed:18042044). Lacks inherent specificity for any particular lysine residue of ubiquitin (PubMed:18042044). Essential for viral activation of IRF3 (PubMed:19854139). Mediates polyubiquitination of CYP3A4 (PubMed:19103148). {ECO:0000269|PubMed:18042044, ECO:0000269|PubMed:18359941, ECO:0000269|PubMed:19103148, ECO:0000269|PubMed:19854139, ECO:0000269|PubMed:20061386, ECO:0000269|PubMed:22496338}.;
- Pathway
- Ubiquitin mediated proteolysis - Homo sapiens (human);Protein processing in endoplasmic reticulum - Homo sapiens (human);Proteasome Degradation;Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha;Regulation of Hypoxia-inducible Factor (HIF) by oxygen;Cellular response to hypoxia;neuroregulin receptor degredation protein-1 controls erbb3 receptor recycling;TICAM1, RIP1-mediated IKK complex recruitment ;Toll Like Receptor 3 (TLR3) Cascade;Toll-Like Receptors Cascades;Senescence-Associated Secretory Phenotype (SASP);Cellular Senescence;Cellular responses to stress;Post-translational protein modification;protein ubiquitylation;Metabolism of proteins;Inactivation of APC/C via direct inhibition of the APC/C complex;Inhibition of the proteolytic activity of APC/C required for the onset of anaphase by mitotic spindle checkpoint components;Mitotic Spindle Checkpoint;Cell Cycle Checkpoints;Synthesis of active ubiquitin: roles of E1 and E2 enzymes;Innate Immune System;Immune System;Adaptive Immune System;Peroxisomal protein import;Antigen processing: Ubiquitination & Proteasome degradation;DNA Replication;Switching of origins to a post-replicative state;Class I MHC mediated antigen processing & presentation;Synthesis of DNA;S Phase;Cellular responses to external stimuli;TGF_beta_Receptor;Neddylation;Ovarian tumor domain proteases;Deubiquitination;Separation of Sister Chromatids;Mitotic Anaphase;Mitotic Metaphase and Anaphase;M Phase;Protein ubiquitination;Regulation of APC/C activators between G1/S and early anaphase;Phosphorylation of the APC/C;CDK-mediated phosphorylation and removal of Cdc6;Cdc20:Phospho-APC/C mediated degradation of Cyclin A;APC-Cdc20 mediated degradation of Nek2A;APC:Cdc20 mediated degradation of cell cycle proteins prior to satisfation of the cell cycle checkpoint;APC/C:Cdc20 mediated degradation of Cyclin B;APC/C:Cdc20 mediated degradation of Securin;APC/C:Cdc20 mediated degradation of mitotic proteins;Activation of APC/C and APC/C:Cdc20 mediated degradation of mitotic proteins;Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase;APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1;Autodegradation of Cdh1 by Cdh1:APC/C;APC/C-mediated degradation of cell cycle proteins;Regulation of mitotic cell cycle;Cell Cycle;IKK complex recruitment mediated by RIP1;TRIF(TICAM1)-mediated TLR4 signaling ;MyD88-independent TLR4 cascade ;Toll Like Receptor 4 (TLR4) Cascade;Cell Cycle, Mitotic;Internalization of ErbB1;E3 ubiquitin ligases ubiquitinate target proteins;p53 pathway
(Consensus)
Recessive Scores
- pRec
- 0.559
Intolerance Scores
- loftool
- rvis_EVS
- 0.04
- rvis_percentile_EVS
- 56.25
Haploinsufficiency Scores
- pHI
- 0.924
- hipred
- Y
- hipred_score
- 0.825
- ghis
- 0.575
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.662
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Low | Low |
| Primary Immunodeficiency | Medium | Low | Medium |
| Cancer | Medium | Low | Medium |
Mouse Genome Informatics
- Gene name
- Ube2d1
- Phenotype
Gene ontology
- Biological process
- negative regulation of transcription by RNA polymerase II;protein polyubiquitination;ubiquitin-dependent protein catabolic process;protein targeting to peroxisome;protein ubiquitination;protein deubiquitination;BMP signaling pathway;anaphase-promoting complex-dependent catabolic process;positive regulation of protein ubiquitination;protein K48-linked ubiquitination;regulation of mitotic cell cycle phase transition;positive regulation of protein polyubiquitination
- Cellular component
- ubiquitin ligase complex;nucleoplasm;cytoplasm;cytosol;protein-containing complex
- Molecular function
- ubiquitin-protein transferase activity;protein binding;ATP binding;ubiquitin protein ligase binding;ubiquitin conjugating enzyme activity