UBE2D4
Basic information
Region (hg38): 7:43926435-43956136
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 UBE2D4 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 | 6 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 6 | 0 | 0 |
Variants in UBE2D4
This is a list of pathogenic ClinVar variants found in the UBE2D4 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 7-43942850-T-C | not specified | Uncertain significance (Mar 22, 2023) | ||
| 7-43948645-C-T | not specified | Uncertain significance (Dec 18, 2023) | ||
| 7-43948652-T-G | not specified | Uncertain significance (Feb 07, 2023) | ||
| 7-43948702-G-A | not specified | Uncertain significance (Aug 12, 2022) | ||
| 7-43950601-C-G | not specified | Uncertain significance (Sep 26, 2022) | ||
| 7-43950667-C-T | not specified | Uncertain significance (May 09, 2022) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| UBE2D4 | protein_coding | protein_coding | ENST00000222402 | 7 | 29699 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0000186 | 0.471 | 125718 | 0 | 28 | 125746 | 0.000111 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.924 | 59 | 82.7 | 0.714 | 0.00000430 | 959 |
| Missense in Polyphen | 22 | 27.447 | 0.80156 | 360 | ||
| Synonymous | 0.629 | 30 | 34.7 | 0.864 | 0.00000219 | 274 |
| Loss of Function | 0.511 | 8 | 9.72 | 0.823 | 4.13e-7 | 114 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000145 | 0.000145 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000272 | 0.000272 |
| Finnish | 0.0000924 | 0.0000924 |
| European (Non-Finnish) | 0.0000967 | 0.0000967 |
| Middle Eastern | 0.000272 | 0.000272 |
| South Asian | 0.000131 | 0.000131 |
| Other | 0.000163 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: Accepts ubiquitin from the E1 complex and catalyzes its covalent attachment to other proteins. In vitro able to promote polyubiquitination using all 7 ubiquitin Lys residues, but may prefer 'Lys-11' and 'Lys-48'-linked polyubiquitination. {ECO:0000269|PubMed:20061386}.;
- Pathway
- Ubiquitin mediated proteolysis - Homo sapiens (human);Protein processing in endoplasmic reticulum - Homo sapiens (human);protein ubiquitylation;Immune System;Adaptive Immune System;Antigen processing: Ubiquitination & Proteasome degradation;Class I MHC mediated antigen processing & presentation
(Consensus)
Recessive Scores
- pRec
- 0.113
Intolerance Scores
- loftool
- 0.733
- rvis_EVS
- 0.13
- rvis_percentile_EVS
- 62.74
Haploinsufficiency Scores
- pHI
- 0.179
- hipred
- Y
- hipred_score
- 0.761
- ghis
- 0.502
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.903
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Ube2d2b
- Phenotype
Gene ontology
- Biological process
- ubiquitin-dependent protein catabolic process;protein ubiquitination;protein K29-linked ubiquitination;protein K27-linked ubiquitination;protein K63-linked ubiquitination;protein K48-linked ubiquitination;protein K11-linked ubiquitination;protein K6-linked ubiquitination
- Cellular component
- ubiquitin ligase complex
- Molecular function
- ubiquitin-protein transferase activity;protein binding;ATP binding;ubiquitin protein ligase binding;ubiquitin conjugating enzyme activity