UBE2L3
ubiquitin conjugating enzyme E2 L3, the group of Ubiquitin conjugating enzymes E2
Basic information
Region (hg38): 22:21549447-21624034
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 UBE2L3 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 | 1 | |||||
| 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 | 1 |
Variants in UBE2L3
This is a list of pathogenic ClinVar variants found in the UBE2L3 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 22-21550753-C-T | not specified | Likely benign (Oct 22, 2021) | ||
| 22-21566528-G-C | Benign (Feb 26, 2021) | |||
| 22-21610864-C-G | not specified | Uncertain significance (Nov 22, 2023) | ||
| 22-21611009-C-G | Benign (Jul 15, 2018) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| UBE2L3 | protein_coding | protein_coding | ENST00000458578 | 4 | 74588 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.838 | 0.159 | 0 | 0 | 0 | 0 | 0.00 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.88 | 9 | 82.6 | 0.109 | 0.00000471 | 1382 |
| Missense in Polyphen | 1 | 29.266 | 0.03417 | 423 | ||
| Synonymous | 1.35 | 21 | 30.5 | 0.688 | 0.00000184 | 429 |
| Loss of Function | 2.27 | 0 | 6.00 | 0.00 | 2.52e-7 | 103 |
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 | 0.00 | 0.00 |
| 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: Ubiquitin-conjugating enzyme E2 that specifically acts with HECT-type and RBR family E3 ubiquitin-protein ligases. Does not function with most RING-containing E3 ubiquitin-protein ligases because it lacks intrinsic E3-independent reactivity with lysine: in contrast, it has activity with the RBR family E3 enzymes, such as PRKN and ARIH1, that function like function like RING-HECT hybrids. Accepts ubiquitin from the E1 complex and catalyzes its covalent attachment to other proteins. In vitro catalyzes 'Lys-11'-linked polyubiquitination. Involved in the selective degradation of short-lived and abnormal proteins. Down- regulated during the S-phase it is involved in progression through the cell cycle. Regulates nuclear hormone receptors transcriptional activity. May play a role in myelopoiesis. {ECO:0000269|PubMed:10888878, ECO:0000269|PubMed:15367689, ECO:0000269|PubMed:17003263, ECO:0000269|PubMed:18946090, ECO:0000269|PubMed:19340006, ECO:0000269|PubMed:20061386, ECO:0000269|PubMed:21532592}.;
- Pathway
- Ubiquitin mediated proteolysis - Homo sapiens (human);Parkinson,s disease - Homo sapiens (human);Parkin-Ubiquitin Proteasomal System pathway;Parkinsons Disease Pathway;role of parkin in ubiquitin-proteasomal pathway;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;BARD1 signaling events;E3 ubiquitin ligases ubiquitinate target proteins;Alpha-synuclein signaling
(Consensus)
Recessive Scores
- pRec
- 0.268
Intolerance Scores
- loftool
- rvis_EVS
- 0.15
- rvis_percentile_EVS
- 63.81
Haploinsufficiency Scores
- pHI
- 0.810
- hipred
- Y
- hipred_score
- 0.687
- ghis
- 0.574
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 1.00
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Low | Low |
| Primary Immunodeficiency | Medium | Low | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Ube2l3
- Phenotype
- growth/size/body region 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); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); embryo phenotype;
Gene ontology
- Biological process
- protein polyubiquitination;regulation of transcription, DNA-templated;cellular protein modification process;ubiquitin-dependent protein catabolic process;cell population proliferation;protein ubiquitination;positive regulation of protein ubiquitination;cell cycle phase transition;positive regulation of ubiquitin-protein transferase activity;protein K11-linked ubiquitination;cellular response to steroid hormone stimulus;cellular response to glucocorticoid stimulus;positive regulation of nucleic acid-templated transcription;positive regulation of protein targeting to mitochondrion
- Cellular component
- ubiquitin ligase complex;nucleus;nucleoplasm;cytoplasm;cytosol
- Molecular function
- transcription coactivator activity;RNA binding;ubiquitin-protein transferase activity;protein binding;ATP binding;enzyme binding;ubiquitin protein ligase binding;ubiquitin conjugating enzyme activity;ubiquitin-protein transferase activator activity