SERPINB3
Basic information
Region (hg38): 18:63655196-63661893
Previous symbols: [ "SCC", "SCCA1" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
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.
In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.
Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.
Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
---|---|---|---|---|---|---|
synonymous | 0 | |||||
missense | 20 | 27 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 0 | |||||
non coding | 0 | |||||
Total | 0 | 0 | 20 | 5 | 2 |
Variants in SERPINB3
This is a list of pathogenic ClinVar variants found in the SERPINB3 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
18-63655680-A-G | not specified | Uncertain significance (May 18, 2023) | ||
18-63655686-G-A | not specified | Uncertain significance (Jul 05, 2023) | ||
18-63655709-C-T | not specified | Likely benign (Nov 30, 2022) | ||
18-63655727-G-A | not specified | Uncertain significance (Dec 09, 2023) | ||
18-63655736-C-T | not specified | Uncertain significance (Dec 15, 2022) | ||
18-63655746-C-T | Benign (Apr 18, 2018) | |||
18-63655749-C-T | not specified | Uncertain significance (Dec 22, 2023) | ||
18-63655750-A-T | not specified | Uncertain significance (Dec 22, 2023) | ||
18-63655764-G-A | Benign (Dec 31, 2019) | |||
18-63655767-A-T | not specified | Uncertain significance (Feb 06, 2024) | ||
18-63655788-C-T | not specified | Uncertain significance (Mar 22, 2023) | ||
18-63655815-C-G | not specified | Uncertain significance (Jul 25, 2023) | ||
18-63655875-C-T | not specified | Uncertain significance (Jun 13, 2024) | ||
18-63655898-T-A | not specified | Uncertain significance (Mar 25, 2024) | ||
18-63655916-A-G | not specified | Uncertain significance (Apr 23, 2024) | ||
18-63655988-T-A | not specified | Uncertain significance (Sep 21, 2021) | ||
18-63656005-C-A | not specified | Uncertain significance (Aug 01, 2022) | ||
18-63656021-G-T | not specified | Uncertain significance (Aug 10, 2021) | ||
18-63656892-T-C | not specified | Uncertain significance (May 07, 2024) | ||
18-63656910-T-A | not specified | Uncertain significance (Aug 17, 2021) | ||
18-63656931-G-A | not specified | Likely benign (Jun 21, 2023) | ||
18-63656965-T-A | not specified | Uncertain significance (Mar 23, 2022) | ||
18-63656969-T-C | not specified | Uncertain significance (Mar 24, 2023) | ||
18-63657278-G-A | not specified | Uncertain significance (Oct 26, 2022) | ||
18-63657314-A-G | not specified | Uncertain significance (Apr 23, 2024) |
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