SERPINA3

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

Basic information

Region (hg38): 14:94612384-94624055

Previous symbols: [ "AACT" ]

Links

ENSG00000196136 ∙ NCBI:12 ∙ OMIM:107280 ∙ HGNC:16 ∙ Uniprot:P01011 ∙ 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 SERPINA3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SERPINA3 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				9	8	17
missense			25	11	1	37
nonsense			1			1
start loss						0
frameshift				1		1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				3		3
Total	0	0	26	24	9

Variants in SERPINA3

This is a list of pathogenic ClinVar variants found in the SERPINA3 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-94614436-T-C		SERPINA3-related disorder	Likely benign (Sep 17, 2019)
14-94614458-C-T		not specified	Uncertain significance (Dec 17, 2023)
14-94614466-G-A		ANTICHYMOTRYPSIN SIGNAL PEPTIDE POLYMORPHISM • not specified • SERPINA3-related disorder	Benign (Mar 28, 2016)
14-94614477-C-T			Benign/Likely benign (Mar 01, 2023)
14-94614490-T-G		not specified	Uncertain significance (May 29, 2024)
14-94614511-C-T		not specified	Likely benign (Jul 09, 2021)
14-94614514-C-T		SERPINA3-related disorder	Likely benign (Oct 01, 2023)
14-94614574-G-A		not specified	Uncertain significance (May 23, 2023)
14-94614582-C-T		SERPINA3-related disorder	Likely benign (Sep 09, 2019)
14-94614593-C-A		not specified	Uncertain significance (Jul 19, 2022)
14-94614595-G-A		not specified	Likely benign (Oct 14, 2023)
14-94614599-A-G			Uncertain significance (Apr 01, 2022)
14-94614618-C-T			Benign (May 21, 2018)
14-94614627-G-A			Likely benign (Jun 12, 2018)
14-94614635-T-G		not specified	Uncertain significance (Jun 23, 2023)
14-94614674-T-C		ANTICHYMOTRYPSIN BOCHUM 1	Pathogenic (Sep 01, 1993)
14-94614688-G-T		not specified	Uncertain significance (Jun 30, 2022)
14-94614699-C-T			Benign (Feb 25, 2018)
14-94614744-A-G		not specified • SERPINA3-related disorder	Benign (Mar 28, 2016)
14-94614764-C-T		not specified	Uncertain significance (Dec 19, 2022)
14-94614804-C-T		SERPINA3-related disorder	Likely benign (Feb 22, 2019)
14-94614811-C-G			Uncertain significance (-)
14-94614812-G-A		not specified	Uncertain significance (May 22, 2023)
14-94614821-A-G		not specified	Uncertain significance (Mar 29, 2022)
14-94614848-G-A		not specified	Likely benign (Sep 17, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SERPINA3	protein_coding	protein_coding	ENST00000467132	4	11679

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
8.83e-14	0.00277	125456	1	291	125748	0.00116

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.37	281	223	1.26	0.0000125	2795
Missense in Polyphen		78	60.747	1.284		836
Synonymous	-2.06	120	94.5	1.27	0.00000593	836
Loss of Function	-1.38	17	11.9	1.43	6.02e-7	145

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00239	0.00227
Ashkenazi Jewish	0.00318	0.00318
East Asian	0.000652	0.000653
Finnish	0.00402	0.00403
European (Non-Finnish)	0.00125	0.000703
Middle Eastern	0.000652	0.000653
South Asian	0.000980	0.000948
Other	0.000815	0.000815

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Although its physiological function is unclear, it can inhibit neutrophil cathepsin G and mast cell chymase, both of which can convert angiotensin-1 to the active angiotensin-2. {ECO:0000269|PubMed:2404007}.
• Pathway: Selenium Micronutrient Network;Vitamin B12 Metabolism;Folate Metabolism;Neutrophil degranulation;Innate Immune System;Immune System;Platelet degranulation ;Response to elevated platelet cytosolic Ca2+;Platelet activation, signaling and aggregation;Hemostasis (Consensus)

Recessive Scores

• pRec: 0.384

Intolerance Scores

• loftool: 0.227
• rvis_EVS: -0.42
• rvis_percentile_EVS: 25.73

Haploinsufficiency Scores

• pHI: 0.183
• hipred: N
• hipred_score: 0.123
• ghis: 0.488

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.917

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Serpina3n

Gene ontology

• Biological process: platelet degranulation;acute-phase response;inflammatory response;negative regulation of endopeptidase activity;regulation of lipid metabolic process;maintenance of gastrointestinal epithelium;neutrophil degranulation
• Cellular component: extracellular region;extracellular space;nucleus;platelet alpha granule lumen;secretory granule lumen;azurophil granule lumen;collagen-containing extracellular matrix;extracellular exosome;blood microparticle
• Molecular function: DNA binding;serine-type endopeptidase inhibitor activity;protein binding