UBE2N
ubiquitin conjugating enzyme E2 N, the group of Ubiquitin conjugating enzymes E2
Basic information
Region (hg38): 12:93405673-93441947
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 UBE2N 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 | 3 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 3 | 0 | 0 |
Variants in UBE2N
This is a list of pathogenic ClinVar variants found in the UBE2N region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 12-93410805-T-C | not specified | Uncertain significance (Dec 21, 2021) | ||
| 12-93410815-T-C | not specified | Uncertain significance (Sep 27, 2022) | ||
| 12-93410845-T-C | not specified | Uncertain significance (Jan 23, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| UBE2N | protein_coding | protein_coding | ENST00000318066 | 4 | 36590 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.882 | 0.117 | 0 | 0 | 0 | 0 | 0.00 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.51 | 21 | 86.8 | 0.242 | 0.00000469 | 985 |
| Missense in Polyphen | 3 | 15.644 | 0.19177 | 240 | ||
| Synonymous | 0.373 | 29 | 31.7 | 0.916 | 0.00000181 | 290 |
| Loss of Function | 2.44 | 0 | 6.95 | 0.00 | 2.94e-7 | 88 |
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: The UBE2V1-UBE2N and UBE2V2-UBE2N heterodimers catalyze the synthesis of non-canonical 'Lys-63'-linked polyubiquitin chains. This type of polyubiquitination does not lead to protein degradation by the proteasome. Mediates transcriptional activation of target genes. Plays a role in the control of progress through the cell cycle and differentiation. Plays a role in the error-free DNA repair pathway and contributes to the survival of cells after DNA damage. Acts together with the E3 ligases, HLTF and SHPRH, in the 'Lys-63'-linked poly-ubiquitination of PCNA upon genotoxic stress, which is required for DNA repair. Appears to act together with E3 ligase RNF5 in the 'Lys-63'-linked polyubiquitination of JKAMP thereby regulating JKAMP function by decreasing its association with components of the proteasome and ERAD. Promotes TRIM5 capsid-specific restriction activity and the UBE2V1-UBE2N heterodimer acts in concert with TRIM5 to generate 'Lys-63'-linked polyubiquitin chains which activate the MAP3K7/TAK1 complex which in turn results in the induction and expression of NF-kappa-B and MAPK-responsive inflammatory genes. {ECO:0000269|PubMed:10089880, ECO:0000269|PubMed:14562038, ECO:0000269|PubMed:19269966, ECO:0000269|PubMed:20061386, ECO:0000269|PubMed:21512573}.;
- Pathway
- Ubiquitin mediated proteolysis - Homo sapiens (human);IL-1 signaling pathway;Interleukin-1 Induced Activation of NF-kappa-B;Simplified Depiction of MYD88 Distinct Input-Output Pathway;TLR NFkB;HDR through Homologous Recombination (HR) or Single Strand Annealing (SSA);Toll Like Receptor 7/8 (TLR7/8) Cascade;DNA Repair;Interleukin-17 signaling;Nonhomologous End-Joining (NHEJ);DNA Double-Strand Break Repair;Signaling by Interleukins;TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling;Cytokine Signaling in Immune system;Toll Like Receptor 9 (TLR9) Cascade;MyD88 cascade initiated on plasma membrane;Toll Like Receptor 10 (TLR10) Cascade;TICAM1, RIP1-mediated IKK complex recruitment ;Toll Like Receptor 3 (TLR3) Cascade;Toll Like Receptor 5 (TLR5) Cascade;B cell receptor signaling;Toll-Like Receptors Cascades;Downstream TCR signaling;TCR signaling;Homology Directed Repair;NOD1/2 Signaling Pathway;Nucleotide-binding domain, leucine rich repeat containing receptor (NLR) signaling pathways;Post-translational protein modification;protein ubiquitylation;Metabolism of proteins;Interleukin-1 signaling;G2/M DNA damage checkpoint;G2/M Checkpoints;IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation;Cell Cycle Checkpoints;Innate Immune System;Immune System;Adaptive Immune System;Antigen processing: Ubiquitination & Proteasome degradation;IL-1 NFkB;Class I MHC mediated antigen processing & presentation;IL-1 p38;IL-1 JNK;IL1;TLR p38;TAK1 activates NFkB by phosphorylation and activation of IKKs complex;JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1;activated TAK1 mediates p38 MAPK activation;MAP kinase activation;TRAF6 mediated induction of NFkB and MAP kinases upon TLR7/8 or 9 activation;MyD88 dependent cascade initiated on endosome;Protein ubiquitination;Cell Cycle;TLR JNK;IKK complex recruitment mediated by RIP1;TRIF(TICAM1)-mediated TLR4 signaling ;MyD88-independent TLR4 cascade ;Toll Like Receptor 4 (TLR4) Cascade;Formation of Incision Complex in GG-NER;Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks;DNA Double Strand Break Response;Global Genome Nucleotide Excision Repair (GG-NER);IRAK1 recruits IKK complex;MyD88:Mal cascade initiated on plasma membrane;Toll Like Receptor TLR1:TLR2 Cascade;Toll Like Receptor TLR6:TLR2 Cascade;Toll Like Receptor 2 (TLR2) Cascade;ISG15 antiviral mechanism;Antiviral mechanism by IFN-stimulated genes;Interferon Signaling;E3 ubiquitin ligases ubiquitinate target proteins;Processing of DNA double-strand break ends;IL1-mediated signaling events;ATM pathway;Interleukin-1 family signaling;CD4 T cell receptor signaling-NFkB cascade;Nucleotide Excision Repair;CD4 T cell receptor signaling
(Consensus)
Intolerance Scores
- loftool
- 0.417
- rvis_EVS
- -0.01
- rvis_percentile_EVS
- 52.85
Haploinsufficiency Scores
- pHI
- 0.446
- hipred
- Y
- hipred_score
- 0.598
- ghis
- 0.693
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- K
- gene_indispensability_pred
- E
- gene_indispensability_score
- 1.00
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Low | Low | Low |
| Primary Immunodeficiency | Low | Low | Low |
| Cancer | Low | Low | Low |
Mouse Genome Informatics
- Gene name
- Ube2n
- Phenotype
- cellular phenotype; immune system phenotype; normal 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); hematopoietic system phenotype;
Gene ontology
- Biological process
- activation of MAPK activity;double-strand break repair via homologous recombination;DNA double-strand break processing;regulation of DNA repair;postreplication repair;double-strand break repair via nonhomologous end joining;cellular protein modification process;proteolysis;ubiquitin-dependent protein catabolic process;JNK cascade;protein ubiquitination;histone ubiquitination;positive regulation of histone modification;regulation of histone ubiquitination;positive regulation of I-kappaB kinase/NF-kappaB signaling;positive regulation of DNA repair;T cell receptor signaling pathway;positive regulation of NF-kappaB transcription factor activity;positive regulation of ubiquitin-protein transferase activity;nucleotide-binding oligomerization domain containing signaling pathway;interleukin-1-mediated signaling pathway;protein K63-linked ubiquitination
- Cellular component
- ubiquitin ligase complex;fibrillar center;nucleus;nucleoplasm;cytoplasm;cytosol;UBC13-MMS2 complex;protein-containing complex;UBC13-UEV1A complex;extracellular exosome
- Molecular function
- RNA binding;ubiquitin-protein transferase activity;protein binding;ATP binding;ubiquitin protein ligase binding;ubiquitin binding;ubiquitin conjugating enzyme activity