SENP2
protein-codingSUMO specific peptidase 2, the group of SUMO specific peptidases
Gene summary
SUMO1 (UBL1; MIM 601912) is a small ubiquitin-like protein that can be covalently conjugated to other proteins. SENP2 is one of a group of enzymes that process newly synthesized SUMO1 into the conjugatable form and catalyze the deconjugation of SUMO1-containing species.[supplied by OMIM, Apr 2004]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~51.1 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 SENP2 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_021627.3. 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 | 2 | 1 | 3 | |||
| missense | 74 | 1 | 1 | 76 | ||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 1 | 1 | ||||
| splice donor/acceptor (+/-2bp) | 3 | 3 | ||||
| Total | 0 | 0 | 80 | 2 | 1 | 83 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_067640.2 | 17 | MANE Select | |
| Ensembl | ENSP00000296257.5 | 17 | MANE Select | |
| Ensembl | ENSP00000388893.1 | 4 | Standard | |
| Ensembl | ENSP00000399156.1 | 7 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- RNA transport - Homo sapiens (human)
- Wnt signaling pathway - Homo sapiens (human)
- Wnt Signaling Pathway
- SUMO is proteolytically processed
- Post-translational protein modification
Biological Process
- positive regulation of protein phosphorylation
- heart development
- dorsal/ventral axis specification
- protein transport
- Wnt signaling pathway
Molecular Function
- protein binding
- protein domain specific binding
- SUMO-specific endopeptidase activity
- SUMO-specific isopeptidase activity
Cellular Component
- nucleus
- nuclear pore
- nucleoplasm
- cytosol
- PML body
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000296257
- Coding exons
- 17
- Length
- 51056
- Individuals with no LoFs
- 125729
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 12
- Defined
- 125741
- p
- 0.0000477
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.87 | 221 | 314 | 0.703 | 0.0000159 | 3869 |
| Missense (PolyPhen) | 51 | 96.309 | 0.52954 | 1186 | ||
| Synonymous | 0.559 | 100 | 107 | 0.931 | 0.00000523 | 1086 |
| Loss of Function | 4.88 | 6 | 38.8 | 0.155 | 0.00000225 | 445 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000062 | 0.000062 | rare |
| Latino/Admixed American | 0.00014 | 0.00014 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00016 | 0.00011 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000018 | 0.000018 | rare |
| South Asian | 0.000066 | 0.000065 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Protease that catalyzes two essential functions in the SUMO pathway. The first is the hydrolysis of an alpha-linked peptide bond at the C-terminal end of the small ubiquitin-like modifier (SUMO) propeptides, SUMO1, SUMO2 and SUMO3 leading to the mature form of the proteins. The second is the deconjugation of SUMO1, SUMO2 and SUMO3 from targeted proteins, by cleaving an epsilon-linked peptide bond between the C-terminal glycine of the mature SUMO and the lysine epsilon-amino group of the target protein. May down-regulate CTNNB1 levels and thereby modulate the Wnt pathway. Deconjugates SUMO2 from MTA1. Plays a dynamic role in adipogenesis by desumoylating and promoting the stabilization of CEBPB (PubMed:20194620). {ECO:0000250|UniProtKB:Q91ZX6, ECO:0000250|UniProtKB:Q9EQE1, ECO:0000269|PubMed:11896061, ECO:0000269|PubMed:12192048, ECO:0000269|PubMed:20194620, ECO:0000269|PubMed:21965678}.;
Recessive Scores
- pRec
- 0.100
Intolerance Scores
- LoFtool
- 0.263
- RVIS EVS
- -0.14
- RVIS percentile EVS
- 43.57
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- S
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.908
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |