SERPINB2

serpin family B member 2, the group of Serpin peptidase inhibitors

Basic information

Region (hg38): 18:63871691-63903888

Previous symbols: [ "PLANH2", "PAI2" ]

Links

ENSG00000197632 ∙ NCBI:5055 ∙ OMIM:173390 ∙ HGNC:8584 ∙ Uniprot:P05120 ∙ 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 SERPINB2 gene.

• Inborn genetic diseases (15 variants)
• not provided (9 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SERPINB2 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				1	3	4
missense			14	3	2	19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	14	4	5

Variants in SERPINB2

This is a list of pathogenic ClinVar variants found in the SERPINB2 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
18-63891568-G-A		not specified	Uncertain significance (Feb 21, 2024)
18-63895320-C-A		not specified	Uncertain significance (Mar 06, 2023)
18-63895334-G-A			Benign (Dec 31, 2019)
18-63895346-A-C		not specified	Uncertain significance (Jun 24, 2022)
18-63895347-G-C		not specified	Uncertain significance (Feb 22, 2023)
18-63895374-G-A			Benign (Dec 31, 2019)
18-63897124-C-T		not specified	Uncertain significance (Nov 09, 2021)
18-63897207-G-A			Benign (Aug 28, 2018)
18-63897751-T-C		not specified	Uncertain significance (Jun 21, 2021)
18-63901736-G-A			Benign (Dec 31, 2019)
18-63901749-C-T		not specified	Likely benign (Dec 26, 2023)
18-63901872-G-A		not specified	Uncertain significance (Jun 01, 2023)
18-63902411-G-A			Likely benign (Jan 02, 2019)
18-63902429-T-A		not specified	Uncertain significance (Apr 12, 2023)
18-63902432-A-G		not specified	Uncertain significance (Apr 12, 2023)
18-63902437-C-T		not specified	Uncertain significance (Jul 13, 2021)
18-63902438-G-A		not specified	Likely benign (Feb 28, 2024)
18-63902453-T-C		not specified	Uncertain significance (Jul 20, 2022)
18-63902461-A-G		Inborn genetic diseases	Uncertain significance (Apr 13, 2023)
18-63902526-G-A			Benign (Dec 31, 2019)
18-63902544-C-T			Likely benign (Dec 31, 2019)
18-63902944-G-A		not specified	Uncertain significance (Mar 06, 2023)
18-63903067-G-A		not specified	Likely benign (Oct 14, 2023)
18-63903103-T-C		not specified	Uncertain significance (Aug 04, 2023)
18-63903168-G-A			Likely benign (Jul 31, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SERPINB2	protein_coding	protein_coding	ENST00000457692	7	32199

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.38e-12	0.0341	125709	0	32	125741	0.000127

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.773	257	224	1.15	0.0000112	2746
Missense in Polyphen		88	78.934	1.1149		1021
Synonymous	-1.65	99	80.2	1.24	0.00000413	765
Loss of Function	-0.0871	17	16.6	1.02	7.64e-7	222

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000461	0.000453
Ashkenazi Jewish	0.0000995	0.0000992
East Asian	0.0000603	0.0000544
Finnish	0.0000469	0.0000462
European (Non-Finnish)	0.000106	0.000105
Middle Eastern	0.0000603	0.0000544
South Asian	0.000169	0.000163
Other	0.000333	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Inhibits urokinase-type plasminogen activator. The monocyte derived PAI-2 is distinct from the endothelial cell- derived PAI-1.
• Pathway: Complement and coagulation cascades - Homo sapiens (human);Blood Clotting Cascade;Aryl Hydrocarbon Receptor Pathway;Nuclear Receptors Meta-Pathway;Dengue-2 Interactions with Blood Clotting Cascade;Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation;Senescence and Autophagy in Cancer;Dissolution of Fibrin Clot;fibrinolysis pathway;Hemostasis (Consensus)

Recessive Scores

• pRec: 0.374

Intolerance Scores

• loftool: 0.221
• rvis_EVS: 0.2
• rvis_percentile_EVS: 67.36

Haploinsufficiency Scores

• pHI: 0.0951
• hipred: N
• hipred_score: 0.445
• ghis: 0.399

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.808

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	Medium	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High

Mouse Genome Informatics

• Gene name: Serpinb2
• Phenotype: hematopoietic system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); immune system phenotype; growth/size/body region phenotype; muscle phenotype

Gene ontology

• Biological process: negative regulation of endopeptidase activity;interleukin-12-mediated signaling pathway;wound healing;fibrinolysis;negative regulation of apoptotic process
• Cellular component: extracellular region;extracellular space;cytoplasm;plasma membrane
• Molecular function: serine-type endopeptidase inhibitor activity