USP11
Basic information
Region (hg38): X:47232866-47248328
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (48 variants)
- not_provided (18 variants)
- Abnormal_ciliary_motility (1 variants)
- Dynein_arm_defect_of_respiratory_motile_cilia (1 variants)
- Absent_inner_and_outer_dynein_arms (1 variants)
- Bronchiectasis (1 variants)
- USP11-related_disorder (1 variants)
- Abnormal_brain_morphology (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the USP11 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001371072.1. 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 | 15 | |||||
| missense | 46 | 51 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 2 | 46 | 9 | 9 |
Highest pathogenic variant AF is 0.0000140499005
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| USP11 | protein_coding | protein_coding | ENST00000218348 | 21 | 15639 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 1.00 | 0.0000377 | 125510 | 0 | 2 | 125512 | 0.00000797 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 3.57 | 225 | 435 | 0.518 | 0.0000379 | 6324 |
| Missense in Polyphen | 65 | 197.84 | 0.32855 | 2795 | ||
| Synonymous | -0.811 | 194 | 180 | 1.08 | 0.0000159 | 1892 |
| Loss of Function | 5.38 | 2 | 37.6 | 0.0532 | 0.00000283 | 572 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000790 | 0.0000616 |
| 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 | 0.0000526 | 0.0000327 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Protease that can remove conjugated ubiquitin from target proteins and polyubiquitin chains (PubMed:12084015, PubMed:15314155, PubMed:17897950, PubMed:19874889, PubMed:20233726, PubMed:24724799). Inhibits the degradation of target proteins by the proteasome (PubMed:12084015). Cleaves preferentially 'Lys-6' and 'Lys-63'-linked ubiquitin chains. Has lower activity with 'Lys-11' and 'Lys-33'-linked ubiquitin chains, and extremely low activity with 'Lys-27', 'Lys-29' and 'Lys-48'- linked ubiquitin chains (in vitro) (PubMed:24724799). Plays a role in the regulation of pathways leading to NF-kappa-B activation (PubMed:17897950, PubMed:19874889). Plays a role in the regulation of DNA repair after double-stranded DNA breaks (PubMed:15314155, PubMed:20233726). Acts as a chromatin regulator via its association with the Polycomb group (PcG) multiprotein PRC1-like complex; may act by deubiquitinating components of the PRC1-like complex (PubMed:20601937). {ECO:0000269|PubMed:15314155, ECO:0000269|PubMed:17897950, ECO:0000269|PubMed:18408009, ECO:0000269|PubMed:19874889, ECO:0000269|PubMed:20233726, ECO:0000269|PubMed:24724799}.;
- Pathway
- Post-translational protein modification;Metabolism of proteins;Chaperonin-mediated protein folding;Association of TriC/CCT with target proteins during biosynthesis;Ub-specific processing proteases;Protein folding;Deubiquitination;TNFalpha
(Consensus)
Recessive Scores
- pRec
- 0.118
Intolerance Scores
- loftool
- 0.172
- rvis_EVS
- -1.04
- rvis_percentile_EVS
- 7.71
Haploinsufficiency Scores
- pHI
- 0.231
- hipred
- Y
- hipred_score
- 0.771
- ghis
- 0.618
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.594
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Usp11
- Phenotype
- homeostasis/metabolism phenotype; hematopoietic system phenotype; immune system phenotype;
Zebrafish Information Network
- Gene name
- usp11
- Affected structure
- post-vent region
- Phenotype tag
- abnormal
- Phenotype quality
- curled
Gene ontology
- Biological process
- ubiquitin-dependent protein catabolic process;protein deubiquitination
- Cellular component
- nucleus;nucleoplasm;chromosome;cytosol
- Molecular function
- cysteine-type endopeptidase activity;thiol-dependent ubiquitin-specific protease activity;protein binding;thiol-dependent ubiquitinyl hydrolase activity