SERPINB3

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

Basic information

Region (hg38): 18:63655196-63661893

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

Links

ENSG00000057149 ∙ NCBI:6317 ∙ OMIM:600517 ∙ HGNC:10569 ∙ Uniprot:P29508 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

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	4	2	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)
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)
18-63655988-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)
18-63656910-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)
18-63657360-C-G		not specified	Uncertain significance (Sep 06, 2022)
18-63657373-C-T		not specified	Likely benign (Feb 21, 2024)
18-63658581-A-G			Likely benign (Mar 01, 2024)
18-63658582-C-T			Likely benign (Mar 01, 2024)
18-63659434-T-C		not specified	Uncertain significance (Dec 28, 2022)

GnomAD

Source: gnomAD

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: 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

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

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