USP6
Basic information
Region (hg38): 17:5116032-5175034
Previous symbols: [ "HRP1", "TRESMCR" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (176 variants)
- not_provided (13 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the USP6 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001304284.2. 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 | 7 | |||||
missense | 170 | 178 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 1 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
Total | 0 | 0 | 170 | 10 | 6 |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
USP6 | protein_coding | protein_coding | ENST00000574788 | 29 | 58597 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
2.95e-35 | 0.00770 | 124183 | 11 | 1554 | 125748 | 0.00624 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | -0.142 | 792 | 781 | 1.01 | 0.0000439 | 9244 |
Missense in Polyphen | 260 | 278.65 | 0.93308 | 3591 | ||
Synonymous | -0.495 | 299 | 288 | 1.04 | 0.0000165 | 2623 |
Loss of Function | 1.74 | 63 | 79.8 | 0.790 | 0.00000455 | 867 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.0508 | 0.0507 |
Ashkenazi Jewish | 0.000298 | 0.000298 |
East Asian | 0.00158 | 0.00152 |
Finnish | 0.0000925 | 0.0000924 |
European (Non-Finnish) | 0.00360 | 0.00352 |
Middle Eastern | 0.00158 | 0.00152 |
South Asian | 0.00515 | 0.00508 |
Other | 0.00471 | 0.00457 |
dbNSFP
Source:
- Function
- FUNCTION: Deubiquitinase with an ATP-independent isopeptidase activity, cleaving at the C-terminus of the ubiquitin moiety. Catalyzes its own deubiquitination. In vitro, isoform 2, but not isoform 3, shows deubiquitinating activity. Promotes plasma membrane localization of ARF6 and selectively regulates ARF6- dependent endocytic protein trafficking. Is able to initiate tumorigenesis by inducing the production of matrix metalloproteinases following NF-kappa-B activation. {ECO:0000269|PubMed:15509780, ECO:0000269|PubMed:16127172, ECO:0000269|PubMed:20418905}.;
- Disease
- DISEASE: Note=A chromosomal aberration involving USP6 is a common genetic feature of aneurysmal bone cyst, a benign osseous neoplasm. Translocation t(16;17)(q22;p13) with CDH11. The translocation generates a fusion gene in which the strong CDH11 promoter is fused to the entire USP6 coding sequence, resulting in USP6 transcriptional up-regulation (PubMed:15026324). {ECO:0000269|PubMed:15026324}.;
- Pathway
- Arf6 signaling events
(Consensus)
Intolerance Scores
- loftool
- 0.996
- rvis_EVS
- 0.42
- rvis_percentile_EVS
- 76.96
Haploinsufficiency Scores
- pHI
- 0.0483
- hipred
- N
- hipred_score
- 0.309
- ghis
- 0.465
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.423
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | High | High | High |
Primary Immunodeficiency | High | High | High |
Cancer | High | High | High |
Gene ontology
- Biological process
- cellular protein modification process;ubiquitin-dependent protein catabolic process;intracellular protein transport;protein deubiquitination;regulation of vesicle-mediated transport;activation of GTPase activity
- Cellular component
- cytoplasm;lysosome;plasma membrane;recycling endosome
- Molecular function
- nucleic acid binding;cysteine-type endopeptidase activity;thiol-dependent ubiquitin-specific protease activity;GTPase activator activity;protein binding;calmodulin binding;Rab GTPase binding