UBE2B
ubiquitin conjugating enzyme E2 B, the group of Ubiquitin conjugating enzymes E2
Basic information
Region (hg38): 5:134371184-134392108
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 UBE2B 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 UBE2B
This is a list of pathogenic ClinVar variants found in the UBE2B region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 5-134371618-G-C | not provided (-) | |||
| 5-134388396-A-G | not specified | Uncertain significance (Mar 06, 2023) | ||
| 5-134390215-T-TTCC | UBE2B-related disorder | Likely benign (Mar 29, 2019) | ||
| 5-134390343-A-G | not specified | Uncertain significance (Oct 20, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| UBE2B | protein_coding | protein_coding | ENST00000265339 | 6 | 20814 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.197 | 0.794 | 125726 | 0 | 5 | 125731 | 0.0000199 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.18 | 27 | 82.8 | 0.326 | 0.00000383 | 998 |
| Missense in Polyphen | 4 | 31.3 | 0.1278 | 376 | ||
| Synonymous | -1.04 | 36 | 28.9 | 1.25 | 0.00000148 | 270 |
| Loss of Function | 2.24 | 3 | 11.0 | 0.272 | 6.36e-7 | 114 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000544 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00000880 | 0.00000879 |
| Middle Eastern | 0.0000544 | 0.0000544 |
| South Asian | 0.0000988 | 0.0000980 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Accepts ubiquitin from the E1 complex and catalyzes its covalent attachment to other proteins. In association with the E3 enzyme BRE1 (RNF20 and/or RNF40), it plays a role in transcription regulation by catalyzing the monoubiquitination of histone H2B at 'Lys-120' to form H2BK120ub1. H2BK120ub1 gives a specific tag for epigenetic transcriptional activation, elongation by RNA polymerase II, telomeric silencing, and is also a prerequisite for H3K4me and H3K79me formation. In vitro catalyzes 'Lys-11'-, as well as 'Lys-48'- and 'Lys-63'-linked polyubiquitination. Required for postreplication repair of UV-damaged DNA. Associates to the E3 ligase RAD18 to form the UBE2B-RAD18 ubiquitin ligase complex involved in mono-ubiquitination of DNA-associated PCNA on 'Lys- 164'. May be involved in neurite outgrowth. {ECO:0000269|PubMed:16337599, ECO:0000269|PubMed:17108083, ECO:0000269|PubMed:17130289, ECO:0000269|PubMed:1717990, ECO:0000269|PubMed:20061386}.;
- Pathway
- Ubiquitin mediated proteolysis - Homo sapiens (human);Proteasome Degradation;DNA Repair;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;Recognition of DNA damage by PCNA-containing replication complex;Protein ubiquitination;DNA Damage Bypass;E3 ubiquitin ligases ubiquitinate target proteins
(Consensus)
Recessive Scores
- pRec
- 0.163
Intolerance Scores
- loftool
- 0.324
- rvis_EVS
- 0.01
- rvis_percentile_EVS
- 54.63
Haploinsufficiency Scores
- pHI
- 0.520
- hipred
- Y
- hipred_score
- 0.800
- ghis
- 0.612
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.992
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Low | Low | Low |
| Primary Immunodeficiency | Low | Low | Low |
| Cancer | Low | Low | Low |
Mouse Genome Informatics
- Gene name
- Ube2b
- Phenotype
- 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); reproductive 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); homeostasis/metabolism phenotype; cellular phenotype; endocrine/exocrine gland phenotype; growth/size/body region 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);
Gene ontology
- Biological process
- protein polyubiquitination;in utero embryonic development;DNA repair;postreplication repair;maintenance of chromatin silencing;ubiquitin-dependent protein catabolic process;protein monoubiquitination;cellular response to DNA damage stimulus;spermatogenesis;sperm axoneme assembly;response to UV;positive regulation of reciprocal meiotic recombination;protein ubiquitination;negative regulation of histone phosphorylation;histone H2A ubiquitination;response to drug;DNA damage response, detection of DNA damage;negative regulation of apoptotic process;proteasome-mediated ubiquitin-dependent protein catabolic process;negative regulation of cAMP-mediated signaling;meiotic telomere clustering;protein stabilization;chiasma assembly;protein autoubiquitination;histone lysine demethylation;synaptonemal complex organization;protein K63-linked ubiquitination;protein K48-linked ubiquitination;protein K11-linked ubiquitination;positive regulation of canonical Wnt signaling pathway
- Cellular component
- chromatin;nuclear chromatin;XY body;nucleus;nucleoplasm;replication fork;cytoplasm;plasma membrane;HULC complex
- Molecular function
- ubiquitin-protein transferase activity;protein binding;ATP binding;ubiquitin protein ligase binding;ubiquitin conjugating enzyme activity