UBE2I
ubiquitin conjugating enzyme E2 I, the group of Ubiquitin conjugating enzymes E2
Basic information
Region (hg38): 16:1308879-1327018
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not provided (3 variants)
- See cases (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the UBE2I 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 ? | 2 | |||||
| Total | 0 | 0 | 1 | 0 | 3 |
Variants in UBE2I
This is a list of pathogenic ClinVar variants found in the UBE2I region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 16-1314280-T-C | Benign (May 06, 2019) | |||
| 16-1314364-A-G | Benign (May 06, 2019) | |||
| 16-1320302-T-C | Benign (Nov 26, 2018) | |||
| 16-1324744-A-G | See cases | Uncertain significance (Jun 21, 2022) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| UBE2I | protein_coding | protein_coding | ENST00000355803 | 6 | 21472 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.965 | 0.0350 | 125579 | 0 | 1 | 125580 | 0.00000398 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 3.10 | 9 | 93.0 | 0.0967 | 0.00000535 | 1030 |
| Missense in Polyphen | 1 | 23.501 | 0.042551 | 307 | ||
| Synonymous | -2.41 | 60 | 40.5 | 1.48 | 0.00000293 | 287 |
| Loss of Function | 2.99 | 0 | 10.4 | 0.00 | 4.42e-7 | 121 |
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) | 0.00000880 | 0.00000880 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Accepts the ubiquitin-like proteins SUMO1, SUMO2, SUMO3, SUMO4 and SUMO1P1/SUMO5 from the UBLE1A-UBLE1B E1 complex and catalyzes their covalent attachment to other proteins with the help of an E3 ligase such as RANBP2, CBX4 and ZNF451. Can catalyze the formation of poly-SUMO chains. Necessary for sumoylation of FOXL2 and KAT5. Essential for nuclear architecture and chromosome segregation. Sumoylates p53/TP53 at 'Lys-386'. {ECO:0000269|PubMed:11451954, ECO:0000269|PubMed:15809060, ECO:0000269|PubMed:17466333, ECO:0000269|PubMed:19638400, ECO:0000269|PubMed:19744555, ECO:0000269|PubMed:20077568, ECO:0000269|PubMed:26524494, ECO:0000269|PubMed:27211601, ECO:0000269|PubMed:8668529}.;
- Pathway
- Ubiquitin mediated proteolysis - Homo sapiens (human);RNA transport - Homo sapiens (human);MicroRNAs in cancer - Homo sapiens (human);NF-kappa B signaling pathway - Homo sapiens (human);Androgen receptor signaling pathway;TGF-beta Signaling Pathway;HDR through Homologous Recombination (HR) or Single Strand Annealing (SSA);DNA Repair;Gene expression (Transcription);DNA Double-Strand Break Repair;er associated degradation (erad) pathway;Generic Transcription Pathway;Metabolism of lipids;SUMO is transferred from E1 to E2 (UBE2I, UBC9);SUMOylation of DNA damage response and repair proteins;SUMOylation of transcription factors;SUMOylation of transcription cofactors;Homology Directed Repair;SUMOylation of chromatin organization proteins;SUMOylation of RNA binding proteins;Post-translational protein modification;SUMOylation of DNA replication proteins;SUMO E3 ligases SUMOylate target proteins;basic mechanisms of sumoylation;protein ubiquitylation;Metabolism of proteins;RNA Polymerase II Transcription;Metabolism;Processing and activation of SUMO;Metabolism of steroids;AndrogenReceptor;SUMOylation;regulation of transcriptional activity by pml;TGF_beta_Receptor;Vitamin D (calciferol) metabolism;Signaling events mediated by HDAC Class II;Coregulation of Androgen receptor activity;C-MYB transcription factor network;Negative regulation of activity of TFAP2 (AP-2) family transcription factors;Transcriptional regulation by the AP-2 (TFAP2) family of transcription factors;TNFalpha;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);Regulation of cytoplasmic and nuclear SMAD2/3 signaling;Processing of DNA double-strand break ends;Sumoylation by RanBP2 regulates transcriptional repression;Signaling events mediated by HDAC Class I;Nucleotide Excision Repair;Steroid hormones
(Consensus)
Recessive Scores
- pRec
- 0.474
Intolerance Scores
- loftool
- 0.348
- rvis_EVS
- -0.1
- rvis_percentile_EVS
- 46.2
Haploinsufficiency Scores
- pHI
- 0.987
- hipred
- Y
- hipred_score
- 0.762
- ghis
- 0.608
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.544
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Low | Medium |
| Primary Immunodeficiency | Medium | Low | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Ube2i
- 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; embryo phenotype; cellular phenotype;
Zebrafish Information Network
- Gene name
- ube2ib
- Affected structure
- chondrocyte
- Phenotype tag
- abnormal
- Phenotype quality
- increased size
Gene ontology
- Biological process
- negative regulation of transcription by RNA polymerase II;cellular protein modification process;ubiquitin-dependent protein catabolic process;cell cycle;chromosome segregation;regulation of signaling receptor activity;viral process;protein ubiquitination;protein sumoylation;positive regulation of intracellular steroid hormone receptor signaling pathway;positive regulation of I-kappaB kinase/NF-kappaB signaling;proteasome-mediated ubiquitin-dependent protein catabolic process;negative regulation of transcription, DNA-templated;positive regulation of DNA-binding transcription factor activity;cell division;positive regulation of SUMO transferase activity
- Cellular component
- synaptonemal complex;fibrillar center;nucleus;nuclear envelope;nucleoplasm;cytoplasm;cytosol;PML body;dendrite;synapse;transferase complex;sumoylated E2 ligase complex
- Molecular function
- RNA binding;ubiquitin-protein transferase activity;protein binding;ATP binding;protein C-terminus binding;transcription factor binding;SUMO transferase activity;enzyme binding;HLH domain binding;bHLH transcription factor binding;small protein activating enzyme binding;SUMO conjugating enzyme activity;RING-like zinc finger domain binding