SERPINA4

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

Basic information

Region (hg38): 14:94561442-94569913

Previous symbols: [ "PI4" ]

Links

ENSG00000100665 ∙ NCBI:5267 ∙ OMIM:147935 ∙ HGNC:8948 ∙ Uniprot:P29622 ∙ 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 SERPINA4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SERPINA4 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			31	3	1	35
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	31	3	2

Variants in SERPINA4

This is a list of pathogenic ClinVar variants found in the SERPINA4 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-94563552-G-A		not specified	Uncertain significance (Dec 04, 2023)
14-94563681-G-A		not specified	Uncertain significance (Mar 21, 2023)
14-94563681-G-T		not specified	Uncertain significance (Sep 20, 2023)
14-94563717-C-T		not specified	Uncertain significance (Jan 03, 2022)
14-94563753-C-A		not specified	Uncertain significance (Feb 28, 2023)
14-94563775-G-A		not specified	Uncertain significance (Dec 04, 2023)
14-94563822-G-C		not specified	Uncertain significance (Jan 23, 2024)
14-94563825-T-A		not specified	Uncertain significance (Oct 10, 2023)
14-94563828-G-T		not specified	Uncertain significance (Mar 20, 2024)
14-94563841-G-A		not specified	Uncertain significance (Jun 22, 2023)
14-94563868-A-G		not specified	Likely benign (Oct 05, 2023)
14-94563892-C-A		not specified	Uncertain significance (Sep 07, 2022)
14-94563894-C-T			Benign (Apr 20, 2018)
14-94563897-G-A		not specified	Likely benign (Oct 12, 2021)
14-94563901-G-C		not specified	Uncertain significance (May 14, 2024)
14-94563933-T-C		not specified	Likely benign (Dec 21, 2022)
14-94563952-A-G		not specified	Uncertain significance (Jan 26, 2022)
14-94563953-T-A		not specified	Uncertain significance (Jan 29, 2024)
14-94563957-A-G		not specified	Uncertain significance (Feb 11, 2022)
14-94563964-C-A		not specified	Uncertain significance (Feb 15, 2023)
14-94563979-A-G		not specified	Uncertain significance (Dec 19, 2022)
14-94564002-G-A		not specified	Uncertain significance (Mar 23, 2022)
14-94564020-C-G		not specified	Uncertain significance (Jan 24, 2024)
14-94567031-G-C		not specified	Uncertain significance (Jun 22, 2023)
14-94567044-C-T		not specified	Uncertain significance (Jun 11, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SERPINA4	protein_coding	protein_coding	ENST00000557004	4	8823

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.73e-9	0.0941	125552	0	196	125748	0.000780

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.678	277	247	1.12	0.0000149	2814
Missense in Polyphen		86	64.549	1.3323		892
Synonymous	-1.31	127	110	1.16	0.00000741	856
Loss of Function	-0.149	12	11.5	1.05	5.54e-7	143

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000817	0.000817
Ashkenazi Jewish	0.00437	0.00437
East Asian	0.000599	0.000598
Finnish	0.000601	0.000601
European (Non-Finnish)	0.000712	0.000712
Middle Eastern	0.000599	0.000598
South Asian	0.000457	0.000457
Other	0.00114	0.00114

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Inhibits human amidolytic and kininogenase activities of tissue kallikrein. Inhibition is achieved by formation of an equimolar, heat- and SDS-stable complex between the inhibitor and the enzyme, and generation of a small C-terminal fragment of the inhibitor due to cleavage at the reactive site by tissue kallikrein. {ECO:0000269|PubMed:8227002}.
• Pathway: Platelet degranulation ;Response to elevated platelet cytosolic Ca2+;Platelet activation, signaling and aggregation;Hemostasis (Consensus)

Recessive Scores

• pRec: 0.239

Intolerance Scores

• rvis_EVS: -0.75
• rvis_percentile_EVS: 13.58

Haploinsufficiency Scores

• pHI: 0.112
• hipred: N
• hipred_score: 0.112
• ghis: 0.434

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.568

Gene Damage Prediction

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

Gene ontology

• Biological process: platelet degranulation;negative regulation of endopeptidase activity
• Cellular component: extracellular region;extracellular space;platelet dense granule lumen;extracellular exosome
• Molecular function: serine-type endopeptidase inhibitor activity