USP47
protein-codingubiquitin specific peptidase 47, the group of Ubiquitin specific peptidases
Gene summary
Enables WD40-repeat domain binding activity and cysteine-type deubiquitinase activity. Involved in base-excision repair; monoubiquitinated protein deubiquitination; and positive regulation of canonical Wnt signaling pathway. Located in cytoplasm. Part of SCF ubiquitin ligase complex. Is active in nucleus. [provided by Alliance of Genome Resources, Jul 2025]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~120.5 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to USP47 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001282659.2. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | 1 | 2 | |||
| missense | 130 | 1 | 131 | |||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 5 | 5 | ||||
| Total | 0 | 0 | 136 | 2 | 1 | 139 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001269588.1 | 28 | MANE Select | |
| Ensembl | ENSP00000433146.2 | 28 | MANE Select | |
| RefSeq | NP_001317137.1 | 29 | Standard | |
| RefSeq | NP_001359020.1 | 28 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Post-translational protein modification
- Metabolism of proteins
- Ub-specific processing proteases
- Deubiquitination
Biological Process
- base-excision repair
- ubiquitin-dependent protein catabolic process
- cellular response to DNA damage stimulus
- negative regulation of G2/M transition of mitotic cell cycle
- protein deubiquitination
Molecular Function
- cysteine-type endopeptidase activity
- thiol-dependent ubiquitin-specific protease activity
- protein binding
- thiol-dependent ubiquitinyl hydrolase activity
- WD40-repeat domain binding
Cellular Component
- nucleoplasm
- cytoplasm
- cytosol
- SCF ubiquitin ligase complex
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000339865
- Coding exons
- 27
- Length
- 117901
- Individuals with no LoFs
- 124776
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 13
- Defined
- 124789
- p
- 0.0000521
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 2.44 | 489 | 666 | 0.734 | 0.0000334 | 8568 |
| Missense (PolyPhen) | 138 | 273.65 | 0.50429 | 3569 | ||
| Synonymous | 0.586 | 221 | 232 | 0.951 | 0.0000117 | 2267 |
| Loss of Function | 7.34 | 4 | 70.5 | 0.0567 | 0.00000364 | 894 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0.000029 | 0.000029 | rare |
| Ashkenazi Jewish | 0.00011 | 0.000099 | rare |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0.000047 | 0.000046 | rare |
| European (Non-Finnish) | 0.000054 | 0.000053 | rare |
| South Asian | 0.00013 | 0.00013 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Ubiquitin-specific protease that specifically deubiquitinates monoubiquitinated DNA polymerase beta (POLB), stabilizing POLB thereby playing a role in base-excision repair (BER). Acts as a regulator of cell growth and genome integrity. May also indirectly regulate CDC25A expression at a transcriptional level. {ECO:0000269|PubMed:19966869, ECO:0000269|PubMed:21362556}.;
Recessive Scores
- pRec
- 0.110
Intolerance Scores
- LoFtool
- 0.171
- RVIS EVS
- -0.62
- RVIS percentile EVS
- 17.45
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.637
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |