SPINT3

serine peptidase inhibitor, Kunitz type 3

Basic information

Region (hg38): 20:45512460-45515622

Links

ENSG00000101446 ∙ NCBI:10816 ∙ OMIM:613941 ∙ HGNC:11248 ∙ Uniprot:P49223 ∙ 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 SPINT3 gene.

• Inborn genetic diseases (5 variants)
• Bladder exstrophy-epispadias-cloacal extrophy complex (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SPINT3 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			6			6
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	6	0	0

Variants in SPINT3

This is a list of pathogenic ClinVar variants found in the SPINT3 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-45512655-G-T		not specified	Uncertain significance (Jan 22, 2024)
20-45512740-A-G		not specified	Uncertain significance (Dec 19, 2023)
20-45512757-T-C		not specified	Uncertain significance (Sep 16, 2021)
20-45512772-G-A		Bladder exstrophy-epispadias-cloacal extrophy complex	Uncertain significance (-)
20-45512795-C-G		not specified	Uncertain significance (Jan 04, 2022)
20-45512803-T-C		not specified	Uncertain significance (Oct 25, 2022)
20-45512812-C-T		not specified	Uncertain significance (Dec 22, 2023)
20-45515550-C-T		not specified	Uncertain significance (Sep 29, 2022)
20-45515556-T-G		not specified	Uncertain significance (May 24, 2023)
20-45515578-G-C		not specified	Uncertain significance (Jun 27, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SPINT3	protein_coding	protein_coding	ENST00000217428	2	3164

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0173	0.498	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.425	39	47.2	0.826	0.00000261	575
Missense in Polyphen		8	15.649	0.51123		188
Synonymous	1.60	9	17.5	0.514	0.00000102	161
Loss of Function	-0.485	2	1.38	1.44	5.93e-8	15

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: 0.66
• rvis_percentile_EVS: 84.27

Haploinsufficiency Scores

• pHI: 0.000300

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.120

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Spint3

Gene ontology

• Biological process: negative regulation of endopeptidase activity;negative regulation of transforming growth factor beta receptor signaling pathway;extracellular negative regulation of signal transduction
• Cellular component: extracellular region
• Molecular function: serine-type endopeptidase inhibitor activity;receptor antagonist activity;transforming growth factor beta binding