USP3

ubiquitin specific peptidase 3, the group of Ubiquitin specific peptidases

Basic information

Region (hg38): 15:63504511-63594640

Links

ENSG00000140455NCBI:9960OMIM:604728HGNC:12626Uniprot:Q9Y6I4AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the USP3 gene.

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
clinvar
2
missense
30
clinvar
1
clinvar
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)2290050
15-63532660-C-A not specified Uncertain significance (Jun 07, 2023)2558935
15-63537078-C-G not specified Uncertain significance (Oct 10, 2023)3187368
15-63537090-A-G not specified Uncertain significance (Mar 31, 2023)2540421
15-63537150-C-T not specified Uncertain significance (Jul 30, 2024)3187369
15-63553719-C-T not specified Uncertain significance (Aug 09, 2021)2363804
15-63553720-G-T not specified Uncertain significance (Jul 25, 2024)3466847
15-63553726-A-T not specified Uncertain significance (Jun 11, 2024)3331434
15-63553792-T-G not specified Uncertain significance (Aug 20, 2024)3466848
15-63558110-G-C not specified Uncertain significance (Jul 12, 2023)2593496
15-63562905-G-A not specified Uncertain significance (Jun 29, 2022)2298929
15-63562950-A-G not specified Uncertain significance (Oct 29, 2024)3466849
15-63570465-T-C not specified Uncertain significance (May 04, 2023)2543805
15-63570506-G-A not specified Uncertain significance (Feb 28, 2024)3187370
15-63570516-G-C not specified Uncertain significance (Feb 14, 2024)3187371
15-63570533-A-G not specified Uncertain significance (Sep 03, 2024)3466846
15-63570542-G-A not specified Uncertain significance (Dec 06, 2024)3466850
15-63574054-C-A not specified Uncertain significance (Oct 29, 2024)2205965
15-63574069-C-T not specified Uncertain significance (May 02, 2024)3331433
15-63574074-A-G not specified Uncertain significance (Jul 14, 2021)2404617
15-63574078-T-G Neutropenia;Lymphopenia Uncertain significance (-)1679870
15-63574132-G-C not specified Uncertain significance (Dec 19, 2023)3187372
15-63574361-C-T not specified Uncertain significance (Apr 06, 2023)2512992
15-63574385-C-A Benign (Sep 19, 2018)710052
15-63588415-C-T Benign (Apr 04, 2018)712841

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
USP3protein_codingprotein_codingENST00000380324 1590047
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
1.000.000110125741061257470.0000239
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense2.111842840.6480.00001523432
Missense in Polyphen60126.240.475281560
Synonymous-0.4621121061.060.00000615918
Loss of Function4.94130.30.03300.00000137402

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.00006250.0000625
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.00004620.0000462
European (Non-Finnish)0.00002680.0000264
Middle Eastern0.000.00
South Asian0.000.00
Other0.000.00

dbNSFP

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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