USP3

Chr 15

ubiquitin specific peptidase 3

Also known as: SIH003, UBP

NCBI Gene: 9960 ENSG00000140455 UniProt: Q9Y6I4 OMIM: 604728

Enables deubiquitinase activity and histone binding activity. Involved in DNA repair and DNA repair-dependent chromatin remodeling. Located in chromatin and nucleoplasm. [provided by Alliance of Genome Resources, Jun 2026]

OMIM Research

OMIM ResearchGenerating clinical summary…

Active trials

Pubs (1 yr)

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P/LP submissions

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P/LP missense

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LOEUF

LOF

Mechanism· predicted

Some data sources returned errors (1)

gnomad: Error: gnomAD API error: 400

Population Genetics & Constraint

gnomAD

Constraint data not available from gnomAD.

Background carrier burden — how many people carry a rare variant somewhere in USP3?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 110

584 rare PASS variants

Rare truncating (LoF)

1 in 2,900

76 rare PASS variants

Rare synonymous (reference)

1 in 160

258 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for USP3. A background rate for each class, not the frequency of any particular variant; thin-coverage exons undercount.

By genetic ancestry · 9 gnomAD groups · rare = under 0.1% in that group

Group	People	Missense	Truncating
European (non-Finnish)	~556k	1 in 130	1 in 2,400
South Asian	~43k	1 in 130	1 in 990
Remaining (unassigned)	~30k	1 in 120	1 in 5,000
European (Finnish)	~27k	1 in 440	≈ 1 in 8,800
Admixed American	~22k	1 in 130	≈ 1 in 5,000
African / African American	~21k	1 in 110	≈ 1 in 5,900
East Asian	~20k	1 in 240	≈ 1 in 20,000
Ashkenazi Jewish	~13k	1 in 680	≈ 1 in 13,000
Middle Eastern	~2,884	1 in 150	none seen

Each group is summed over the variants that are rare in that group. Grey ≈ figures rest on fewer than five expected carriers — too few to distinguish groups. Differences mostly reflect how many people were sampled and how much variation each ancestry carries, not disease risk.