UBXN1
UBX domain protein 1, the group of UBX domain containing
Basic information
Region (hg38): 11:62676498-62679117
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (41 variants)
- not_provided (3 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the UBXN1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001286077.2. 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 | 2 | |||||
| missense | 35 | 36 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 35 | 3 | 0 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| UBXN1 | protein_coding | protein_coding | ENST00000294119 | 8 | 2598 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.728 | 0.272 | 125739 | 0 | 9 | 125748 | 0.0000358 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.838 | 160 | 193 | 0.830 | 0.0000116 | 1983 |
| Missense in Polyphen | 55 | 77.16 | 0.7128 | 814 | ||
| Synonymous | -1.25 | 82 | 68.8 | 1.19 | 0.00000352 | 637 |
| Loss of Function | 3.20 | 3 | 17.4 | 0.172 | 8.50e-7 | 194 |
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 | 0.0000949 | 0.0000924 |
| European (Non-Finnish) | 0.0000265 | 0.0000264 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000654 | 0.0000653 |
| Other | 0.000326 | 0.000326 |
dbNSFP
Source:
- Function
- FUNCTION: Ubiquitin-binding protein that plays a role in the modulation of innate immune response. Blocks both the RIG-I-like receptors (RLR) and NF-kappa-B pathways. Following viral infection, UBXN1 is induced and recruited to the RLR component MAVS. In turn, interferes with MAVS oligomerization, and disrupts the MAVS/TRAF3/TRAF6 signalosome. This function probably serves as a brake to prevent excessive RLR signaling (PubMed:23545497). Interferes with the TNFalpha-triggered NF-kappa-B pathway by interacting with cellular inhibitors of apoptosis proteins (cIAPs) and thereby inhibiting their recruitment to TNFR1 (PubMed:25681446). Prevents also the activation of NF-kappa-B by associating with CUL1 and thus inhibiting NF-kappa-B inhibitor alpha/NFKBIA degradation that remains bound to NF-kappa-B (PubMed:28152074). Interacts with the BRCA1-BARD1 heterodimer and regulates its activity. Specifically binds 'Lys-6'-linked polyubiquitin chains. Interaction with autoubiquitinated BRCA1 leads to the inhibition of the E3 ubiquitin-protein ligase activity of the BRCA1-BARD1 heterodimer (PubMed:20351172). Component of a complex required to couple deglycosylation and proteasome-mediated degradation of misfolded proteins in the endoplasmic reticulum that are retrotranslocated in the cytosol. {ECO:0000269|PubMed:20351172, ECO:0000269|PubMed:23545497, ECO:0000269|PubMed:25681446, ECO:0000269|PubMed:28152074}.;
- Pathway
- Post-translational protein modification;Metabolism of proteins;Asparagine N-linked glycosylation;N-glycan trimming in the ER and Calnexin/Calreticulin cycle
(Consensus)
Recessive Scores
- pRec
- 0.118
Intolerance Scores
- loftool
- 0.415
- rvis_EVS
- 0.48
- rvis_percentile_EVS
- 79.04
Haploinsufficiency Scores
- pHI
- hipred
- Y
- hipred_score
- 0.701
- ghis
- 0.404
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.567
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Ubxn1
- Phenotype
Gene ontology
- Biological process
- protein folding;viral process;negative regulation of protein ubiquitination;negative regulation of proteasomal ubiquitin-dependent protein catabolic process;proteasome-mediated ubiquitin-dependent protein catabolic process;negative regulation of protein K48-linked deubiquitination;negative regulation of ERAD pathway;negative regulation of ubiquitin-specific protease activity
- Cellular component
- nucleus;cytoplasm;endoplasmic reticulum;cytosol;dendrite;VCP-NPL4-UFD1 AAA ATPase complex;neuronal cell body
- Molecular function
- protein binding;polyubiquitin modification-dependent protein binding;ubiquitin protein ligase binding;K48-linked polyubiquitin modification-dependent protein binding;ubiquitin binding;ATPase binding;K6-linked polyubiquitin modification-dependent protein binding;proteasome regulatory particle binding