USP29
protein-codingubiquitin specific peptidase 29, the group of Ubiquitin specific peptidases
Gene summary
Predicted to enable cysteine-type deubiquitinase activity and cysteine-type endopeptidase activity. Predicted to be involved in several processes, including G1/S transition of mitotic cell cycle; positive regulation of type I interferon-mediated signaling pathway; and protein K48-linked deubiquitination. Located in plasma membrane. [provided by Alliance of Genome Resources, Jun 2026]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~12.8 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 USP29 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_020903.3. 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 | 9 | 139 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 130 | 10 | 1 | 141 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_065954.1 | 1 | MANE Select | |
| Ensembl | ENSP00000254181.3 | 1 | MANE Select | |
| RefSeq | NP_001376572.1 | 1 | Standard | |
| Ensembl | ENSP00000470747.1 | 1 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- G1/S transition of mitotic cell cycle
- ubiquitin-dependent protein catabolic process
- protein deubiquitination
Molecular Function
- cysteine-type endopeptidase activity
- thiol-dependent ubiquitin-specific protease activity
- thiol-dependent ubiquitinyl hydrolase activity
Cellular Component
- cellular_component
- nucleus
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000254181
- Coding exons
- 1
- Length
- 12789
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.0823 | 460 | 465 | 0.989 | 0.0000213 | 6157 |
| Missense (PolyPhen) | 87 | 103.9 | 0.83735 | 1487 | ||
| Synonymous | 0.0686 | 176 | 177 | 0.993 | 0.00000863 | 1711 |
| Loss of Function |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0 | 0.0 | absent |
| South Asian | 0 | 0.0 | absent |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
Recessive Scores
- pRec
- 0.0718
Intolerance Scores
- LoFtool
- 0.743
- RVIS EVS
- 1.67
- RVIS percentile EVS
- 96.33
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.565
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |