SERPINE3
protein-codingserpin family E member 3, the group of Serpin peptidase inhibitors
Gene summary
Predicted to enable serine-type endopeptidase inhibitor activity. Predicted to be located in extracellular region. Predicted to be active in obsolete extracellular space. [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 ~29.0 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 SERPINE3 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001386375.1. 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 | 0 | |||||
| missense | 39 | 7 | 46 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 39 | 7 | 0 | 46 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001373304.1 | 8 | MANE Select | |
| Ensembl | ENSP00000506411.1 | 8 | MANE Select | |
| RefSeq | NP_001094790.1 | 7 | Standard | |
| Ensembl | ENSP00000441468.1 | 8 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- negative regulation of endopeptidase activity
Molecular Function
- serine-type endopeptidase inhibitor activity
Cellular Component
- extracellular space
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000521255
- Coding exons
- 7
- Length
- 28963
- Individuals with no LoFs
- 124600
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 55
- Defined
- 124655
- p
- 0.000221
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.970 | 188 | 229 | 0.820 | 0.0000120 | 2767 |
| Missense (PolyPhen) | 52 | 66.467 | 0.78234 | 932 | ||
| Synonymous | 0.432 | 88 | 93.3 | 0.943 | 0.00000524 | 846 |
| Loss of Function | 1.22 | 11 | 16.3 | 0.674 | 8.66e-7 | 174 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00035 | 0.00032 | rare |
| Latino/Admixed American | 0.00032 | 0.00032 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.000056 | 0.000056 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.00024 | 0.00019 | rare |
| South Asian | 0.00034 | 0.00033 | rare |
| Other | 0.0010 | 0.00099 | notable |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Probable serine protease inhibitor. {ECO:0000250}.;
Intolerance Scores
- LoFtool
- 0.536
- RVIS EVS
- 0.11
- RVIS percentile EVS
- 61.91
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.114
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |