UBE2S
ubiquitin conjugating enzyme E2 S, the group of Ubiquitin conjugating enzymes E2
Basic information
Region (hg38): 19:55399745-55407788
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (36 variants)
- not_provided (7 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the UBE2S gene is commonly pathogenic or not. These statistics are base on transcript: NM_000014501.3. 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 | 6 | |||||
| missense | 33 | 34 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 33 | 4 | 3 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| UBE2S | protein_coding | protein_coding | ENST00000264552 | 4 | 6494 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.632 | 0.362 | 125525 | 0 | 2 | 125527 | 0.00000797 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.959 | 121 | 155 | 0.783 | 0.0000105 | 1410 |
| Missense in Polyphen | 27 | 60.342 | 0.44745 | 605 | ||
| Synonymous | -1.18 | 88 | 75.0 | 1.17 | 0.00000579 | 492 |
| Loss of Function | 2.19 | 1 | 7.45 | 0.134 | 4.01e-7 | 85 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000289 | 0.0000289 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00 | 0.00 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000327 | 0.0000327 |
| 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). Catalyzes 'Lys-11'-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 specifically elongating 'Lys-11'-linked polyubiquitin chains initiated by the E2 enzyme UBE2C/UBCH10 on APC/C substrates, enhancing the degradation of APC/C substrates by the proteasome and promoting mitotic exit (PubMed:19820702, PubMed:19822757, PubMed:27259151). Also acts by elongating ubiquitin chains initiated by the E2 enzyme UBE2D1/UBCH5 in vitro; it is however unclear whether UBE2D1/UBCH5 acts as an E2 enzyme for the APC/C in vivo. Also involved in ubiquitination and subsequent degradation of VHL, resulting in an accumulation of HIF1A (PubMed:16819549). In vitro able to promote polyubiquitination using all 7 ubiquitin Lys residues, except 'Lys-48'-linked polyubiquitination (PubMed:20061386, PubMed:20622874). {ECO:0000269|PubMed:16819549, ECO:0000269|PubMed:19820702, ECO:0000269|PubMed:19822757, ECO:0000269|PubMed:20061386, ECO:0000269|PubMed:20622874, ECO:0000269|PubMed:22496338, ECO:0000269|PubMed:27259151}.;
- Pathway
- Ubiquitin mediated proteolysis - Homo sapiens (human);miR-targeted genes in epithelium - TarBase;miR-targeted genes in lymphocytes - TarBase;Post-translational protein modification;protein ubiquitylation;Metabolism of proteins;Synthesis of active ubiquitin: roles of E1 and E2 enzymes;Immune System;Adaptive Immune System;Antigen processing: Ubiquitination & Proteasome degradation;Class I MHC mediated antigen processing & presentation;Protein ubiquitination
(Consensus)
Recessive Scores
- pRec
- 0.122
Intolerance Scores
- loftool
- 0.194
- rvis_EVS
- -0.25
- rvis_percentile_EVS
- 35.42
Haploinsufficiency Scores
- pHI
- 0.341
- hipred
- Y
- hipred_score
- 0.815
- ghis
- 0.694
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.968
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Ube2s
- Phenotype
Gene ontology
- Biological process
- cellular protein modification process;ubiquitin-dependent protein catabolic process;exit from mitosis;free ubiquitin chain polymerization;protein ubiquitination;anaphase-promoting complex-dependent catabolic process;protein K29-linked ubiquitination;protein K27-linked ubiquitination;cell division;protein K63-linked ubiquitination;protein K11-linked ubiquitination;protein K6-linked ubiquitination;positive regulation of ubiquitin protein ligase activity
- Cellular component
- nucleoplasm;anaphase-promoting complex;cytosol
- Molecular function
- ubiquitin-protein transferase activity;protein binding;ATP binding;anaphase-promoting complex binding;ubiquitin conjugating enzyme activity