SERPINB3
serpin family B member 3, the group of Serpin peptidase inhibitors
Basic information
Region (hg38): 18:63655196-63661893
Previous symbols: [ "SCC", "SCCA1" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- Inborn genetic diseases (10 variants)
- not provided (2 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the SERPINB3 gene is commonly pathogenic or not.
| Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 9 | 1 | 2 | 12 | ||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice variant | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 9 | 1 | 2 |
Variants in SERPINB3
This is a list of pathogenic ClinVar variants found in the SERPINB3 region.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 18-63655680-A-G | Inborn genetic diseases | Uncertain significance (May 18, 2023) | ||
| 18-63655686-G-A | Inborn genetic diseases | Uncertain significance (Jul 05, 2023) | ||
| 18-63655709-C-T | Inborn genetic diseases | Likely benign (Nov 30, 2022) | ||
| 18-63655736-C-T | Inborn genetic diseases | Uncertain significance (Dec 15, 2022) | ||
| 18-63655746-C-T | Benign (Apr 18, 2018) | |||
| 18-63655764-G-A | Benign (Dec 31, 2019) | |||
| 18-63655788-C-T | Inborn genetic diseases | Uncertain significance (Mar 22, 2023) | ||
| 18-63655815-C-G | Inborn genetic diseases | Uncertain significance (Jul 25, 2023) | ||
| 18-63655988-T-A | Inborn genetic diseases | Uncertain significance (Sep 21, 2021) | ||
| 18-63656021-G-T | Inborn genetic diseases | Uncertain significance (Aug 10, 2021) | ||
| 18-63656910-T-A | Inborn genetic diseases | Uncertain significance (Aug 17, 2021) | ||
| 18-63656931-G-A | Inborn genetic diseases | Likely benign (Jun 21, 2023) | ||
| 18-63656965-T-A | Inborn genetic diseases | Uncertain significance (Mar 23, 2022) | ||
| 18-63656969-T-C | Inborn genetic diseases | Uncertain significance (Mar 24, 2023) | ||
| 18-63657278-G-A | Inborn genetic diseases | Uncertain significance (Oct 26, 2022) | ||
| 18-63657360-C-G | Inborn genetic diseases | Uncertain significance (Sep 06, 2022) | ||
| 18-63659434-T-C | Inborn genetic diseases | Uncertain significance (Dec 28, 2022) | ||
| 18-63659487-A-G | Inborn genetic diseases | Uncertain significance (Dec 05, 2022) | ||
| 18-63661134-A-G | Inborn genetic diseases | Uncertain significance (Aug 15, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| SERPINB3 | protein_coding | protein_coding | ENST00000283752 | 7 | 6767 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 8.21e-16 | 0.00126 | 125331 | 4 | 384 | 125719 | 0.00154 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | -1.66 | 277 | 209 | 1.32 | 0.0000108 | 2580 |
| Missense in 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 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000489 | 0.000489 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000600 | 0.000599 |
| Finnish | 0.0000464 | 0.0000462 |
| European (Non-Finnish) | 0.000373 | 0.000369 |
| Middle Eastern | 0.000600 | 0.000599 |
| South Asian | 0.0106 | 0.0105 |
| Other | 0.000654 | 0.000652 |
dbNSFP
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}.;
- Pathway
- Amoebiasis - Homo sapiens (human);Neutrophil degranulation;Innate Immune System;Immune System;EGFR1
(Consensus)
Recessive Scores
- pRec
- 0.318
Intolerance Scores
- loftool
- 0.210
- rvis_EVS
- 2.18
- rvis_percentile_EVS
- 98.07
Haploinsufficiency Scores
- pHI
- 0.317
- hipred
- N
- hipred_score
- 0.112
- ghis
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.708
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Serpinb3d
- Phenotype
Gene ontology
- 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;positive regulation of cell migration;autocrine signaling;paracrine signaling;negative regulation of catalytic activity;neutrophil degranulation;negative regulation of JUN kinase activity;negative regulation of proteolysis;viral entry into host cell
- Cellular component
- extracellular region;extracellular space;nucleus;cytoplasm;cytoplasmic vesicle;vesicle;azurophil granule lumen;extracellular exosome
- Molecular function
- virus receptor activity;protease binding;serine-type endopeptidase inhibitor activity;cysteine-type endopeptidase inhibitor activity