UBE2W
Basic information
Region (hg38): 8:73780097-73878910
Links
Phenotypes
GenCC
Source:
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 UBE2W 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 | 2 | |||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 0 | |||||
non coding | 0 | |||||
Total | 0 | 0 | 2 | 0 | 0 |
Variants in UBE2W
This is a list of pathogenic ClinVar variants found in the UBE2W region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
8-73810557-G-C | not specified | Uncertain significance (Jan 29, 2024) | ||
8-73810626-T-C | not specified | Uncertain significance (Dec 27, 2023) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
UBE2W | protein_coding | protein_coding | ENST00000419880 | 7 | 98814 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.0924 | 0.900 | 117288 | 179 | 7155 | 124622 | 0.0299 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 1.81 | 43 | 91.8 | 0.468 | 0.00000416 | 1225 |
Missense in Polyphen | 7 | 31.657 | 0.22112 | 418 | ||
Synonymous | -0.111 | 32 | 31.2 | 1.03 | 0.00000151 | 349 |
Loss of Function | 2.33 | 4 | 13.1 | 0.305 | 7.86e-7 | 145 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.0305 | 0.0304 |
Ashkenazi Jewish | 0.0580 | 0.0579 |
East Asian | 0.0000559 | 0.0000556 |
Finnish | 0.0292 | 0.0288 |
European (Non-Finnish) | 0.0460 | 0.0455 |
Middle Eastern | 0.0000559 | 0.0000556 |
South Asian | 0.00178 | 0.00177 |
Other | 0.0345 | 0.0340 |
dbNSFP
Source:
- Function
- FUNCTION: Accepts ubiquitin from the E1 complex and catalyzes its covalent attachment to other proteins (PubMed:20061386, PubMed:21229326). Specifically monoubiquitinates the N-terminus of various substrates, including ATXN3, MAPT/TAU, POLR2H/RPB8 and STUB1/CHIP, by recognizing backbone atoms of disordered N-termini (PubMed:23560854, PubMed:23696636, PubMed:25436519). Involved in degradation of misfolded chaperone substrates by mediating monoubiquitination of STUB1/CHIP, leading to recruitment of ATXN3 to monoubiquitinated STUB1/CHIP, and restriction of the length of ubiquitin chain attached to STUB1/CHIP substrates by ATXN3. After UV irradiation, but not after mitomycin-C (MMC) treatment, 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:19111657, PubMed:21229326). In vitro catalyzes 'Lys-11'-linked polyubiquitination. UBE2W-catalyzed ubiquitination occurs also in the presence of inactive RING/U-box type E3s, i.e. lacking the active site cysteine residues to form thioester bonds with ubiquitin, or even in the absence of E3, albeit at a slower rate (PubMed:25436519). {ECO:0000269|PubMed:19111657, ECO:0000269|PubMed:20061386, ECO:0000269|PubMed:21229326, ECO:0000269|PubMed:23560854, ECO:0000269|PubMed:23696636, ECO:0000269|PubMed:25436519}.;
- Pathway
- Ubiquitin mediated proteolysis - Homo sapiens (human);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
- 0.0945
Intolerance Scores
- loftool
- rvis_EVS
- 0.12
- rvis_percentile_EVS
- 62.38
Haploinsufficiency Scores
- pHI
- 0.634
- hipred
- Y
- hipred_score
- 0.712
- ghis
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.443
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Ube2w
- Phenotype
- endocrine/exocrine gland phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); cellular phenotype; immune system 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); reproductive system phenotype; hematopoietic system phenotype; hearing/vestibular/ear phenotype;
Gene ontology
- Biological process
- DNA repair;protein monoubiquitination;protein quality control for misfolded or incompletely synthesized proteins;protein ubiquitination;proteasome-mediated ubiquitin-dependent protein catabolic process;protein K11-linked ubiquitination;cellular response to misfolded protein
- Cellular component
- nucleus;nucleoplasm
- Molecular function
- ubiquitin-protein transferase activity;protein binding;ATP binding;ubiquitin protein ligase binding;ubiquitin conjugating enzyme activity