UBE2C
ubiquitin conjugating enzyme E2 C, the group of Ubiquitin conjugating enzymes E2
Basic information
Region (hg38): 20:45812576-45816957
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 UBE2C 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 | 5 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 5 | 0 | 0 |
Variants in UBE2C
This is a list of pathogenic ClinVar variants found in the UBE2C region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 20-45813453-A-G | not specified | Uncertain significance (Mar 20, 2023) | ||
| 20-45815583-A-G | not specified | Uncertain significance (Mar 24, 2023) | ||
| 20-45815641-A-T | not specified | Uncertain significance (Dec 16, 2023) | ||
| 20-45815911-C-T | not specified | Uncertain significance (Mar 01, 2023) | ||
| 20-45816761-G-T | not specified | Uncertain significance (Oct 05, 2021) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| UBE2C | protein_coding | protein_coding | ENST00000356455 | 6 | 4382 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.105 | 0.867 | 125733 | 0 | 15 | 125748 | 0.0000596 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.505 | 86 | 100 | 0.858 | 0.00000487 | 1151 |
| Missense in Polyphen | 13 | 25.957 | 0.50082 | 360 | ||
| Synonymous | 1.56 | 31 | 44.1 | 0.702 | 0.00000250 | 355 |
| Loss of Function | 1.88 | 3 | 9.14 | 0.328 | 3.86e-7 | 110 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000906 | 0.0000906 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000109 | 0.0000544 |
| Finnish | 0.0000924 | 0.0000924 |
| European (Non-Finnish) | 0.0000879 | 0.0000879 |
| Middle Eastern | 0.000109 | 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. In vitro catalyzes 'Lys- 11'- and 'Lys-48'-linked polyubiquitination. Acts as an essential factor of the anaphase promoting complex/cyclosome (APC/C), a cell cycle-regulated ubiquitin ligase that controls progression through mitosis. Acts by initiating 'Lys-11'-linked polyubiquitin chains on APC/C substrates, leading to the degradation of APC/C substrates by the proteasome and promoting mitotic exit. {ECO:0000269|PubMed:15558010, ECO:0000269|PubMed:18485873, ECO:0000269|PubMed:19820702, ECO:0000269|PubMed:19822757, ECO:0000269|PubMed:20061386, ECO:0000269|PubMed:27259151}.;
- Pathway
- Ubiquitin mediated proteolysis - Homo sapiens (human);Gastric Cancer Network 1;Gastric Cancer Network 2;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;Immune System;Adaptive Immune System;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;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;Cell Cycle, Mitotic
(Consensus)
Recessive Scores
- pRec
- 0.234
Intolerance Scores
- loftool
- 0.873
- rvis_EVS
- -0.25
- rvis_percentile_EVS
- 35.42
Haploinsufficiency Scores
- pHI
- 0.991
- hipred
- Y
- hipred_score
- 0.682
- ghis
- 0.655
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.995
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Ube2c
- 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); growth/size/body region phenotype; vision/eye phenotype; embryo phenotype;
Gene ontology
- Biological process
- ubiquitin-dependent protein catabolic process;exit from mitosis;free ubiquitin chain polymerization;protein ubiquitination;anaphase-promoting complex-dependent catabolic process;positive regulation of exit from mitosis;cell division;protein K48-linked ubiquitination;protein K11-linked ubiquitination;regulation of mitotic cell cycle phase transition;positive regulation of ubiquitin protein ligase activity
- Cellular component
- ubiquitin ligase complex;nucleus;nucleoplasm;anaphase-promoting complex;cytosol;plasma membrane
- Molecular function
- ubiquitin-protein transferase activity;protein binding;ATP binding;ubiquitin-like protein ligase binding;ubiquitin conjugating enzyme activity