SERPINB3
protein-codingserpin family B member 3, the group of Serpin peptidase inhibitors
Gene summary
Enables cysteine-type endopeptidase inhibitor activity and protease binding activity. Located in cytoplasmic vesicle; extracellular exosome; and nucleus. Is active in cytosol. [provided by Alliance of Genome Resources, Jun 2026]
- SCC
- SCCA1
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~6.7 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 SERPINB3 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_006919.3. 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 | ||||
| missense | 57 | 10 | 2 | 69 | ||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 0 | 0 | 58 | 11 | 2 | 71 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_008850.1 | 7 | MANE Select | |
| Ensembl | ENSP00000283752.5 | 7 | MANE Select | |
| Ensembl | ENSP00000329498.8 | 6 | Standard | |
| Ensembl | ENSP00000329498.8 | 6 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Amoebiasis - Homo sapiens (human)
- Neutrophil degranulation
- Innate Immune System
- Immune System
- EGFR1
Biological Process
- positive regulation of cell population proliferation
- negative regulation of peptidase activity
- positive regulation of epithelial to mesenchymal transition
- positive regulation of endopeptidase activity
- negative regulation of endopeptidase activity
Molecular Function
- virus receptor activity
- protease binding
- serine-type endopeptidase inhibitor activity
- cysteine-type endopeptidase inhibitor activity
Cellular Component
- extracellular region
- extracellular space
- nucleus
- cytoplasm
- cytoplasmic vesicle
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000283752
- Coding exons
- 7
- Length
- 6767
- Individuals with no LoFs
- 125331
- Homozygous LoFs
- 4
- Heterozygous LoFs
- 384
- Defined
- 125719
- p
- 0.00154
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -1.66 | 277 | 209 | 1.32 | 0.0000108 | 2580 |
| Missense (PolyPhen) | 78 | 60.765 | 1.2836 | 833 | ||
| Synonymous | -2.28 | 110 | 83.5 | 1.32 | 0.00000488 | 703 |
| Loss of Function | -1.28 | 20 | 14.7 | 1.36 | 6.84e-7 | 183 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00043 | 0.00043 | rare |
| Latino/Admixed American | 0.000058 | 0.000058 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00060 | 0.00060 | rare |
| Finnish | 0.000046 | 0.000046 | rare |
| European (Non-Finnish) | 0.00037 | 0.00037 | rare |
| South Asian | 0.011 | 0.011 | notable |
| Other | 0.00065 | 0.00065 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: May act as a papain-like cysteine protease inhibitor to modulate the host immune response against tumor cells. Also functions as an inhibitor of UV-induced apoptosis via suppression of the activity of c-Jun NH(2)-terminal kinase (JNK1). {ECO:0000269|PubMed:19166818}.;
Recessive Scores
- pRec
- 0.318
Intolerance Scores
- LoFtool
- 0.210
- RVIS EVS
- 2.18
- RVIS percentile EVS
- 98.07
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.708
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |