SERPINB4

serpin family B member 4, the group of Serpin peptidase inhibitors

Basic information

Region (hg38): 18:63637258-63644256

Previous symbols: [ "SCCA2" ]

Links

ENSG00000206073 ∙ NCBI:6318 ∙ OMIM:600518 ∙ HGNC:10570 ∙ Uniprot:P48594 ∙ 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 SERPINB4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SERPINB4 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			25	2		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	25	2	0

Variants in SERPINB4

This is a list of pathogenic ClinVar variants found in the SERPINB4 region.

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

Position	Type	Phenotype	Significance	ClinVar
18-63637765-T-C		not specified	Uncertain significance (Apr 22, 2022)
18-63637773-T-C		not specified	Uncertain significance (Dec 05, 2022)
18-63637802-A-G		not specified	Uncertain significance (Jun 29, 2023)
18-63637975-T-C		not specified	Uncertain significance (Jul 11, 2022)
18-63637976-T-C		not specified	Likely benign (Dec 18, 2023)
18-63637976-T-G		not specified	Uncertain significance (Feb 16, 2023)
18-63637999-G-C		not specified	Uncertain significance (Jan 03, 2022)
18-63639286-A-T		not specified	Uncertain significance (Aug 02, 2022)
18-63639293-A-T		not specified	Uncertain significance (Feb 23, 2023)
18-63639317-C-A		not specified	Uncertain significance (Feb 13, 2023)
18-63639318-A-G		not specified	Uncertain significance (Nov 27, 2023)
18-63639643-C-G		not specified	Uncertain significance (Feb 22, 2023)
18-63639644-C-A		not specified	Uncertain significance (Feb 22, 2023)
18-63639663-T-C		not specified	Uncertain significance (Sep 14, 2022)
18-63639677-A-G		not specified	Uncertain significance (Jun 07, 2023)
18-63639683-T-C		not specified	Uncertain significance (Jun 29, 2022)
18-63639714-T-G		not specified	Uncertain significance (Dec 02, 2022)
18-63639731-G-A		not specified	Uncertain significance (Dec 02, 2022)
18-63639743-A-G		not specified	Uncertain significance (Feb 17, 2024)
18-63639756-G-T		not specified	Uncertain significance (May 31, 2023)
18-63639761-A-G		not specified	Uncertain significance (Apr 07, 2022)
18-63639770-A-T		Malignant tumor of prostate	Uncertain significance (-)
18-63640982-C-T		not specified	Uncertain significance (Oct 17, 2023)
18-63641786-C-T		not specified	Uncertain significance (Jan 30, 2024)
18-63641822-C-T		not specified	Uncertain significance (Jan 03, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SERPINB4	protein_coding	protein_coding	ENST00000341074	7	7040

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
8.76e-17	0.000649	125324	0	385	125709	0.00153

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.87	279	204	1.37	0.00000994	2604
Missense in Polyphen		86	67.139	1.2809		913
Synonymous	-3.14	115	79.4	1.45	0.00000447	685
Loss of Function	-1.46	21	14.9	1.41	6.95e-7	182

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00670	0.00666
Ashkenazi Jewish	0.000696	0.000695
East Asian	0.000109	0.000109
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.00152	0.00151
Middle Eastern	0.000109	0.000109
South Asian	0.000266	0.000261
Other	0.00213	0.00212

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May act as a protease inhibitor to modulate the host immune response against tumor cells.
• Pathway: Amoebiasis - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.117

Intolerance Scores

• loftool: 0.235
• rvis_EVS: -0.33
• rvis_percentile_EVS: 30.7

Haploinsufficiency Scores

• pHI: 0.0704
• hipred: N
• hipred_score: 0.112
• ghis: 0.419

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.534

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: negative regulation of peptidase activity;negative regulation of endopeptidase activity;regulation of proteolysis;protection from natural killer cell mediated cytotoxicity
• Cellular component: extracellular space;cytoplasm
• Molecular function: protease binding;serine-type endopeptidase inhibitor activity;enzyme binding