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.

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	2
missense			30		1	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: 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