SERPINB1

serpin family B member 1, the group of Serpin peptidase inhibitors

Basic information

Region (hg38): 6:2832331-2841959

Previous symbols: [ "ELANH2" ]

Links

ENSG00000021355 ∙ NCBI:1992 ∙ OMIM:130135 ∙ HGNC:3311 ∙ Uniprot:P30740 ∙ 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 SERPINB1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SERPINB1 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	1
missense			20	2	2	24
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding					1	1
Total	0	0	20	2	4

Variants in SERPINB1

This is a list of pathogenic ClinVar variants found in the SERPINB1 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-2833778-C-T		not specified	Uncertain significance (Apr 23, 2024)
6-2833871-C-T		not specified	Uncertain significance (Aug 02, 2022)
6-2833879-C-T		not specified	Uncertain significance (Apr 12, 2024)
6-2833880-G-A			Benign (May 08, 2018)
6-2833925-T-C		not specified	Uncertain significance (Nov 18, 2022)
6-2833948-A-G		not specified	Uncertain significance (Sep 20, 2022)
6-2833960-T-G		not specified	Uncertain significance (Aug 14, 2023)
6-2833967-G-A		not specified	Uncertain significance (Apr 20, 2023)
6-2833981-T-C		not specified	Likely benign (Sep 21, 2023)
6-2835875-T-G		not specified	Uncertain significance (Oct 10, 2023)
6-2835893-G-A		not specified	Uncertain significance (May 26, 2024)
6-2835910-G-C		not specified	Uncertain significance (Oct 12, 2022)
6-2835956-A-T		not specified	Uncertain significance (Sep 16, 2021)
6-2835960-C-T		not specified	Uncertain significance (Jun 21, 2022)
6-2835982-T-G		not specified	Uncertain significance (Oct 20, 2023)
6-2836032-T-A			Benign (Apr 11, 2019)
6-2836133-G-A		not specified	Uncertain significance (Feb 05, 2024)
6-2836221-T-C		not specified	Likely benign (Aug 10, 2023)
6-2836226-G-A		not specified	Uncertain significance (Aug 13, 2021)
6-2836252-T-TA			Benign (Feb 20, 2018)
6-2837904-C-G		not specified	Uncertain significance (Jun 11, 2021)
6-2837966-C-T		not specified	Uncertain significance (Apr 24, 2024)
6-2837971-T-C		not specified	Uncertain significance (Jan 31, 2023)
6-2838604-T-C		not specified	Uncertain significance (Nov 16, 2022)
6-2838607-G-A		not specified	Uncertain significance (Aug 13, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SERPINB1	protein_coding	protein_coding	ENST00000380739	6	9675

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.55e-8	0.192	125723	0	25	125748	0.0000994

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.794	178	210	0.846	0.0000115	2509
Missense in Polyphen		43	62.575	0.68717		841
Synonymous	0.348	85	89.2	0.953	0.00000570	715
Loss of Function	0.258	12	13.0	0.923	5.44e-7	182

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000183	0.000183
Ashkenazi Jewish	0.00	0.00
East Asian	0.000217	0.000217
Finnish	0.0000926	0.0000924
European (Non-Finnish)	0.0000977	0.0000879
Middle Eastern	0.000217	0.000217
South Asian	0.0000654	0.0000653
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Regulates the activity of the neutrophil proteases elastase, cathepsin G, proteinase-3, chymase, chymotrypsin, and kallikrein-3. Also functions as a potent intracellular inhibitor of granzyme H. {ECO:0000269|PubMed:11747453}.
• Pathway: Amoebiasis - Homo sapiens (human);Vitamin D Receptor Pathway;Neutrophil degranulation;Innate Immune System;Immune System (Consensus)

Recessive Scores

• pRec: 0.652

Intolerance Scores

• loftool: 0.290
• rvis_EVS: 0.02
• rvis_percentile_EVS: 55.61

Haploinsufficiency Scores

• pHI: 0.128
• hipred: N
• hipred_score: 0.190
• ghis: 0.446

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.734

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Serpinb1c

Gene ontology

• Biological process: negative regulation of endopeptidase activity;neutrophil degranulation
• Cellular component: extracellular region;extracellular space;membrane;secretory granule lumen;collagen-containing extracellular matrix;extracellular exosome
• Molecular function: serine-type endopeptidase inhibitor activity