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GeneBe

SERPINB3

serpin family B member 3, the group of Serpin peptidase inhibitors

Basic information

Region (hg38): 18:63655196-63661893

Previous symbols: [ "SCC", "SCCA1" ]

Links

ENSG00000057149NCBI:6317OMIM:600517HGNC:10569Uniprot:P29508AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SERPINB3 gene.

  • Inborn genetic diseases (17 variants)
  • not provided (4 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.

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
15
clinvar
4
clinvar
2
clinvar
21
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 0 0 15 4 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)2549276
18-63655686-G-A not specified Uncertain significance (Jul 05, 2023)2594843
18-63655709-C-T not specified Likely benign (Nov 30, 2022)2295145
18-63655727-G-A not specified Uncertain significance (Dec 09, 2023)3160414
18-63655736-C-T not specified Uncertain significance (Dec 15, 2022)2335468
18-63655746-C-T Benign (Apr 18, 2018)774727
18-63655749-C-T not specified Uncertain significance (Dec 22, 2023)3160413
18-63655750-A-T not specified Uncertain significance (Dec 22, 2023)3160412
18-63655764-G-A Benign (Dec 31, 2019)768937
18-63655767-A-T not specified Uncertain significance (Feb 06, 2024)3160411
18-63655788-C-T not specified Uncertain significance (Mar 22, 2023)2528569
18-63655815-C-G not specified Uncertain significance (Jul 25, 2023)2614332
18-63655988-T-A not specified Uncertain significance (Sep 21, 2021)2232010
18-63656005-C-A not specified Uncertain significance (Aug 01, 2022)3160418
18-63656021-G-T not specified Uncertain significance (Aug 10, 2021)2381665
18-63656910-T-A not specified Uncertain significance (Aug 17, 2021)2246507
18-63656931-G-A not specified Likely benign (Jun 21, 2023)2599003
18-63656965-T-A not specified Uncertain significance (Mar 23, 2022)2279526
18-63656969-T-C not specified Uncertain significance (Mar 24, 2023)2520979
18-63657278-G-A not specified Uncertain significance (Oct 26, 2022)2361735
18-63657360-C-G not specified Uncertain significance (Sep 06, 2022)2310510
18-63657373-C-T not specified Likely benign (Feb 21, 2024)3160416
18-63658581-A-G Likely benign (Dec 01, 2023)2648793
18-63658582-C-T Likely benign (Apr 01, 2023)2648794
18-63659434-T-C not specified Uncertain significance (Dec 28, 2022)2340106

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SERPINB3protein_codingprotein_codingENST00000283752 76767
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
8.21e-160.0012612533143841257190.00154
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-1.662772091.320.00001082580
Missense in Polyphen7860.7651.2836833
Synonymous-2.2811083.51.320.00000488703
Loss of Function-1.282014.71.366.84e-7183

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0004890.000489
Ashkenazi Jewish0.000.00
East Asian0.0006000.000599
Finnish0.00004640.0000462
European (Non-Finnish)0.0003730.000369
Middle Eastern0.0006000.000599
South Asian0.01060.0105
Other0.0006540.000652

dbNSFP

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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