SERPINE3

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

Basic information

Region (hg38): 13:51335773-51364735

Links

ENSG00000253309 ∙ NCBI:647174 ∙ ∙ HGNC:24774 ∙ Uniprot:A8MV23 ∙ 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 SERPINE3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SERPINE3 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			22	4		26
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	22	4	0

Variants in SERPINE3

This is a list of pathogenic ClinVar variants found in the SERPINE3 region.

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

Position	Type	Phenotype	Significance	ClinVar
13-51341096-C-T		not specified	Likely benign (Jul 09, 2021)
13-51341158-C-T		not specified	Uncertain significance (Nov 27, 2023)
13-51341169-G-T		not specified	Uncertain significance (May 06, 2022)
13-51341180-A-G		not specified	Uncertain significance (Mar 22, 2023)
13-51341191-G-T		not specified	Uncertain significance (Dec 12, 2024)
13-51341272-C-G		not specified	Uncertain significance (Apr 13, 2022)
13-51341293-G-A		not specified	Uncertain significance (Aug 02, 2022)
13-51344260-G-T		not specified	Uncertain significance (Dec 28, 2024)
13-51344273-T-C		not specified	Uncertain significance (Mar 13, 2023)
13-51344281-G-C		not specified	Uncertain significance (Apr 08, 2024)
13-51344317-G-A		not specified	Likely benign (May 10, 2024)
13-51344357-C-T		not specified	Uncertain significance (Jun 07, 2023)
13-51344386-G-A		not specified	Uncertain significance (Mar 22, 2023)
13-51344461-G-A		not specified	Uncertain significance (Nov 21, 2022)
13-51347058-C-T		not specified	Uncertain significance (Feb 13, 2025)
13-51347099-G-C		not specified	Uncertain significance (Aug 12, 2022)
13-51347174-T-C		not specified	Uncertain significance (May 23, 2023)
13-51347198-G-C		not specified	Uncertain significance (Dec 16, 2023)
13-51347205-T-G		not specified	Uncertain significance (Jan 22, 2024)
13-51347217-C-T		not specified	Likely benign (Sep 08, 2024)
13-51348248-G-A		not specified	Uncertain significance (Jun 29, 2023)
13-51348275-G-T		not specified	Uncertain significance (Apr 17, 2023)
13-51348287-T-C		not specified	Likely benign (Mar 05, 2024)
13-51348381-G-A		not specified	Likely benign (Mar 07, 2025)
13-51348399-T-C		not specified	Uncertain significance (Dec 07, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SERPINE3	protein_coding	protein_coding	ENST00000521255	7	28963

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000250	0.753	124600	0	55	124655	0.000221

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.970	188	229	0.820	0.0000120	2767
Missense in Polyphen		52	66.467	0.78234		932
Synonymous	0.432	88	93.3	0.943	0.00000524	846
Loss of Function	1.22	11	16.3	0.674	8.66e-7	174

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000678	0.000646
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000560	0.0000556
Finnish	0.00	0.00
European (Non-Finnish)	0.000238	0.000195
Middle Eastern	0.0000560	0.0000556
South Asian	0.000336	0.000327
Other	0.00104	0.000991

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probable serine protease inhibitor. {ECO:0000250}.

Intolerance Scores

• loftool: 0.536
• rvis_EVS: 0.11
• rvis_percentile_EVS: 61.91

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.144

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Serpine3

Gene ontology

• Biological process: negative regulation of endopeptidase activity
• Cellular component: extracellular space
• Molecular function: serine-type endopeptidase inhibitor activity