UBD
ubiquitin D
Basic information
Region (hg38): 6:29555515-29559732
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (17 variants)
- not_provided (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the UBD gene is commonly pathogenic or not. These statistics are base on transcript: NM_000006398.4. Only rare variants are included in the table.
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.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 14 | 18 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 14 | 4 | 0 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| UBD | protein_coding | protein_coding | ENST00000377050 | 2 | 4411 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.00705 | 0.547 | 123379 | 1 | 54 | 123434 | 0.000223 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.236 | 85 | 91.3 | 0.931 | 0.00000489 | 1066 |
| Missense in Polyphen | 23 | 23.841 | 0.96471 | 331 | ||
| Synonymous | 0.418 | 33 | 36.2 | 0.912 | 0.00000200 | 326 |
| Loss of Function | 0.0758 | 3 | 3.15 | 0.954 | 1.31e-7 | 48 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00134 | 0.00134 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000903 | 0.0000902 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000329 | 0.0000329 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Ubiquitin-like protein modifier which can be covalently attached to target protein and subsequently leads to their degradation by the 26S proteasome, in a NUB1-dependent manner. Probably functions as a survival factor. Conjugation ability activated by UBA6. Promotes the expression of the proteasome subunit beta type-9 (PSMB9/LMP2). Regulates TNF-alpha-induced and LPS-mediated activation of the central mediator of innate immunity NF-kappa-B by promoting TNF-alpha-mediated proteasomal degradation of ubiquitinated-I-kappa-B-alpha. Required for TNF-alpha-induced p65 nuclear translocation in renal tubular epithelial cells (RTECs). May be involved in dendritic cell (DC) maturation, the process by which immature dendritic cells differentiate into fully competent antigen-presenting cells that initiate T-cell responses. Mediates mitotic non-disjunction and chromosome instability, in long-term in vitro culture and cancers, by abbreviating mitotic phase and impairing the kinetochore localization of MAD2L1 during the prometaphase stage of the cell cycle. May be involved in the formation of aggresomes when proteasome is saturated or impaired. Mediates apoptosis in a caspase-dependent manner, especially in renal epithelium and tubular cells during renal diseases such as polycystic kidney disease and Human immunodeficiency virus (HIV)- associated nephropathy (HIVAN). {ECO:0000269|PubMed:15831455, ECO:0000269|PubMed:16495226, ECO:0000269|PubMed:16495380, ECO:0000269|PubMed:17889673, ECO:0000269|PubMed:18574467, ECO:0000269|PubMed:19028597, ECO:0000269|PubMed:19033385, ECO:0000269|PubMed:19166848, ECO:0000269|PubMed:19726511, ECO:0000269|PubMed:19959714}.;
- Pathway
- Post-translational protein modification;Metabolism of proteins;Neddylation
(Consensus)
Intolerance Scores
- loftool
- 0.501
- rvis_EVS
- 1.66
- rvis_percentile_EVS
- 96.23
Haploinsufficiency Scores
- pHI
- hipred
- Y
- hipred_score
- 0.581
- ghis
- 0.528
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.543
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | High |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Ubd
- Phenotype
- cellular phenotype; immune system phenotype; hematopoietic system phenotype;
Gene ontology
- Biological process
- proteolysis;ubiquitin-dependent protein catabolic process;protein ubiquitination;protein modification by small protein conjugation;response to interferon-gamma;response to tumor necrosis factor;myeloid dendritic cell differentiation;positive regulation of apoptotic process;positive regulation of I-kappaB kinase/NF-kappaB signaling;post-translational protein modification;aggresome assembly;regulation of mitotic cell cycle phase transition
- Cellular component
- fibrillar center;nucleus;cytoplasm;cytosol;aggresome
- Molecular function
- protein binding;proteasome binding