USP3

ubiquitin specific peptidase 3, the group of Ubiquitin specific peptidases

Basic information

Region (hg38): 15:63504511-63594640

Links

ENSG00000140455

∙ NCBI:9960 ∙ OMIM:604728 ∙ HGNC:12626 ∙ Uniprot:Q9Y6I4 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

not_specified (45 variants)
not_provided (3 variants)
Decreased_total_neutrophil_count (1 variants)
Decreased_total_lymphocyte_count (1 variants)

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. These statistics are base on transcript: NM_000006537.4. 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					2 clinvar	2
missense			46 clinvar		1 clinvar	47
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	46	0	3

Loading clinvar variants...

GnomAD

Source: gnomAD

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: 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

	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