USP3
Basic information
Region (hg38): 15:63504511-63594640
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the USP3 gene is commonly pathogenic or not.
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.
Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
---|---|---|---|---|---|---|
synonymous | 2 | |||||
missense | 30 | 31 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 0 | |||||
non coding | 0 | |||||
Total | 0 | 0 | 30 | 0 | 3 |
Variants in USP3
This is a list of pathogenic ClinVar variants found in the USP3 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
15-63504780-C-A | not specified | Uncertain significance (May 18, 2022) | ||
15-63532660-C-A | not specified | Uncertain significance (Jun 07, 2023) | ||
15-63537078-C-G | not specified | Uncertain significance (Oct 10, 2023) | ||
15-63537090-A-G | not specified | Uncertain significance (Mar 31, 2023) | ||
15-63537150-C-T | not specified | Uncertain significance (Jul 30, 2024) | ||
15-63553719-C-T | not specified | Uncertain significance (Aug 09, 2021) | ||
15-63553720-G-T | not specified | Uncertain significance (Jul 25, 2024) | ||
15-63553726-A-T | not specified | Uncertain significance (Jun 11, 2024) | ||
15-63553792-T-G | not specified | Uncertain significance (Aug 20, 2024) | ||
15-63558110-G-C | not specified | Uncertain significance (Jul 12, 2023) | ||
15-63562905-G-A | not specified | Uncertain significance (Jun 29, 2022) | ||
15-63562950-A-G | not specified | Uncertain significance (Oct 29, 2024) | ||
15-63570465-T-C | not specified | Uncertain significance (May 04, 2023) | ||
15-63570506-G-A | not specified | Uncertain significance (Feb 28, 2024) | ||
15-63570516-G-C | not specified | Uncertain significance (Feb 14, 2024) | ||
15-63570533-A-G | not specified | Uncertain significance (Sep 03, 2024) | ||
15-63570542-G-A | not specified | Uncertain significance (Dec 06, 2024) | ||
15-63574054-C-A | not specified | Uncertain significance (Oct 29, 2024) | ||
15-63574069-C-T | not specified | Uncertain significance (May 02, 2024) | ||
15-63574074-A-G | not specified | Uncertain significance (Jul 14, 2021) | ||
15-63574078-T-G | Neutropenia;Lymphopenia | Uncertain significance (-) | ||
15-63574132-G-C | not specified | Uncertain significance (Dec 19, 2023) | ||
15-63574361-C-T | not specified | Uncertain significance (Apr 06, 2023) | ||
15-63574385-C-A | Benign (Sep 19, 2018) | |||
15-63588415-C-T | Benign (Apr 04, 2018) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
USP3 | protein_coding | protein_coding | ENST00000380324 | 15 | 90047 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
1.00 | 0.000110 | 125741 | 0 | 6 | 125747 | 0.0000239 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 2.11 | 184 | 284 | 0.648 | 0.0000152 | 3432 |
Missense in Polyphen | 60 | 126.24 | 0.47528 | 1560 | ||
Synonymous | -0.462 | 112 | 106 | 1.06 | 0.00000615 | 918 |
Loss of Function | 4.94 | 1 | 30.3 | 0.0330 | 0.00000137 | 402 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.0000625 | 0.0000625 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.00 | 0.00 |
Finnish | 0.0000462 | 0.0000462 |
European (Non-Finnish) | 0.0000268 | 0.0000264 |
Middle Eastern | 0.00 | 0.00 |
South Asian | 0.00 | 0.00 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Hydrolase that deubiquitinates monoubiquitinated target proteins such as histone H2A and H2B. Required for proper progression through S phase and subsequent mitotic entry. May regulate the DNA damage response (DDR) checkpoint through deubiquitination of H2A at DNA damage sites. Associates with the chromatin. {ECO:0000269|PubMed:17980597}.;
- Pathway
- Post-translational protein modification;Metabolism of proteins;Ub-specific processing proteases;Deubiquitination
(Consensus)
Recessive Scores
- pRec
- 0.111
Intolerance Scores
- loftool
- 0.316
- rvis_EVS
- -0.43
- rvis_percentile_EVS
- 25.37
Haploinsufficiency Scores
- pHI
- 0.247
- hipred
- Y
- hipred_score
- 0.783
- ghis
- 0.584
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.924
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Usp3
- 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);
Zebrafish Information Network
- Gene name
- usp3
- Affected structure
- caudal fin upper lobe
- Phenotype tag
- abnormal
- Phenotype quality
- fused with
Gene ontology
- Biological process
- negative regulation of transcription by RNA polymerase II;mitotic cell cycle;DNA repair;ubiquitin-dependent protein catabolic process;histone deubiquitination;protein deubiquitination;regulation of protein stability
- Cellular component
- nuclear chromatin;nucleus;nucleoplasm;cytoplasm;cytoplasmic ribonucleoprotein granule;Flemming body
- Molecular function
- RNA polymerase II proximal promoter sequence-specific DNA binding;thiol-dependent ubiquitin-specific protease activity;zinc ion binding;thiol-dependent ubiquitinyl hydrolase activity;histone binding;promoter-specific chromatin binding