USP16
Basic information
Region (hg38): 21:29024629-29054488
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (90 variants)
- not_provided (2 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the USP16 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000006447.3. 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 | 1 | |||||
| missense | 89 | 90 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 89 | 1 | 1 |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| USP16 | protein_coding | protein_coding | ENST00000334352 | 17 | 29860 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 1.85e-9 | 0.998 | 125653 | 0 | 95 | 125748 | 0.000378 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.350 | 399 | 419 | 0.952 | 0.0000205 | 5505 |
| Missense in Polyphen | 137 | 177.44 | 0.77208 | 2405 | ||
| Synonymous | 1.29 | 126 | 146 | 0.865 | 0.00000747 | 1430 |
| Loss of Function | 2.83 | 21 | 40.4 | 0.520 | 0.00000186 | 559 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00103 | 0.00103 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000115 | 0.000109 |
| Finnish | 0.0000467 | 0.0000462 |
| European (Non-Finnish) | 0.000322 | 0.000316 |
| Middle Eastern | 0.000115 | 0.000109 |
| South Asian | 0.000824 | 0.000752 |
| Other | 0.000326 | 0.000326 |
dbNSFP
Source:
- Function
- FUNCTION: Specifically deubiquitinates 'Lys-120' of histone H2A (H2AK119Ub), a specific tag for epigenetic transcriptional repression, thereby acting as a coactivator. Deubiquitination of histone H2A is a prerequisite for subsequent phosphorylation at 'Ser-11' of histone H3 (H3S10ph), and is required for chromosome segregation when cells enter into mitosis. In resting B- and T- lymphocytes, phosphorylation by AURKB leads to enhance its activity, thereby maintaining transcription in resting lymphocytes. Regulates Hox gene expression via histone H2A deubiquitination. Prefers nucleosomal substrates. Does not deubiquitinate histone H2B. {ECO:0000255|HAMAP-Rule:MF_03062, ECO:0000269|PubMed:10077596, ECO:0000269|PubMed:17914355}.;
- Disease
- DISEASE: Note=A chromosomal aberration involving USP16 is a cause of Chronic myelomonocytic leukemia. Inversion inv(21) (q21;q22) with RUNX1/AML1.;
- Pathway
- Post-translational protein modification;Metabolism of proteins;Ub-specific processing proteases;Deubiquitination
(Consensus)
Recessive Scores
- pRec
- 0.108
Intolerance Scores
- loftool
- 0.981
- rvis_EVS
- -0.09
- rvis_percentile_EVS
- 47.06
Haploinsufficiency Scores
- pHI
- 0.235
- hipred
- Y
- hipred_score
- 0.637
- ghis
- 0.586
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.621
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Usp16
- 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);
Gene ontology
- Biological process
- mitotic cell cycle;regulation of transcription by RNA polymerase II;ubiquitin-dependent protein catabolic process;cellular response to DNA damage stimulus;histone deubiquitination;protein deubiquitination;monoubiquitinated histone H2A deubiquitination;positive regulation of transcription, DNA-templated;positive regulation of translational elongation;positive regulation of transcription by RNA polymerase II;protein homotetramerization;cell division;regulation of cell cycle;histone H2A K63-linked deubiquitination;mitotic nuclear division
- Cellular component
- nucleus;nucleoplasm;cytoplasm
- Molecular function
- transcription coactivator activity;cysteine-type endopeptidase activity;thiol-dependent ubiquitin-specific protease activity;zinc ion binding;thiol-dependent ubiquitinyl hydrolase activity;histone binding;ubiquitin binding