SPINT1

serine peptidase inhibitor, Kunitz type 1

Basic information

Region (hg38): 15:40844018-40858207

Links

ENSG00000166145 ∙ NCBI:6692 ∙ OMIM:605123 ∙ HGNC:11246 ∙ Uniprot:O43278 ∙ 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 SPINT1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SPINT1 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			53	6	3	62
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	53	6	3

Variants in SPINT1

This is a list of pathogenic ClinVar variants found in the SPINT1 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-40844571-C-G		not specified	Uncertain significance (Dec 19, 2023)
15-40844624-C-T		not specified	Uncertain significance (Jan 12, 2024)
15-40844664-C-T		not specified	Uncertain significance (Jun 29, 2022)
15-40844678-C-T		not specified	Uncertain significance (Mar 04, 2025)
15-40844720-G-T		not specified	Uncertain significance (Nov 22, 2022)
15-40844742-T-C		not specified	Uncertain significance (Apr 07, 2022)
15-40844753-G-T		not specified	Uncertain significance (Nov 07, 2022)
15-40844781-T-A		not specified	Uncertain significance (Aug 27, 2024)
15-40844820-G-A		not specified	Uncertain significance (Jan 20, 2025)
15-40844822-G-A		not specified	Uncertain significance (Sep 17, 2021)
15-40844835-C-T		not specified	Uncertain significance (Jan 21, 2025)
15-40844861-G-A		not specified	Uncertain significance (Nov 15, 2021)
15-40844915-T-A		not specified	Uncertain significance (Dec 19, 2023)
15-40844969-A-G		not specified	Uncertain significance (Dec 16, 2023)
15-40844988-T-C		not specified	Uncertain significance (Sep 24, 2024)
15-40844991-A-T		not specified	Uncertain significance (Apr 12, 2024)
15-40845000-A-G		not specified	Uncertain significance (Apr 27, 2024)
15-40845007-G-T		not specified	Uncertain significance (Apr 27, 2024)
15-40853141-G-T		not specified	Uncertain significance (Feb 08, 2025)
15-40853142-C-T		not specified	Uncertain significance (Feb 23, 2023)
15-40853217-G-A		not specified	Likely benign (Dec 28, 2023)
15-40853225-C-T		not specified	Uncertain significance (Jun 23, 2023)
15-40853235-C-T		not specified	Uncertain significance (Feb 14, 2023)
15-40853568-A-G		not specified	Uncertain significance (Oct 05, 2021)
15-40853616-A-C		not specified	Uncertain significance (Nov 22, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SPINT1	protein_coding	protein_coding	ENST00000344051	10	14190

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000102	0.987	125629	0	119	125748	0.000473

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0731	322	326	0.989	0.0000186	3445
Missense in Polyphen		81	92.185	0.87866		1065
Synonymous	0.749	125	136	0.918	0.00000801	1065
Loss of Function	2.24	12	23.8	0.505	0.00000102	271

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00247	0.00247
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.000140	0.000139
European (Non-Finnish)	0.000256	0.000255
Middle Eastern	0.0000544	0.0000544
South Asian	0.000165	0.000163
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Inhibitor of HGF activator. Also acts as an inhibitor of matriptase (ST14).
• Pathway: Prostate cancer - Homo sapiens (human);Transcriptional misregulation in cancer - Homo sapiens (human);Signal Transduction;MET Receptor Activation;Signaling by MET;Signaling by MST1;Signaling by Receptor Tyrosine Kinases (Consensus)

Recessive Scores

• pRec: 0.169

Intolerance Scores

• loftool: 0.148
• rvis_EVS: 0.27
• rvis_percentile_EVS: 70.73

Haploinsufficiency Scores

• pHI: 0.163
• hipred: N
• hipred_score: 0.199
• ghis: 0.496

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.908

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Spint1
• Phenotype: integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); growth/size/body region phenotype; endocrine/exocrine gland phenotype; cellular phenotype; homeostasis/metabolism phenotype; digestive/alimentary phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); embryo phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); immune system phenotype; limbs/digits/tail phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan)

Zebrafish Information Network

• Gene name: spint1a
• Affected structure: neutrophil
• Phenotype tag: abnormal
• Phenotype quality: mislocalised

Gene ontology

• Biological process: neural tube closure;negative regulation of endopeptidase activity;extracellular matrix organization;positive regulation of glial cell differentiation;branching involved in labyrinthine layer morphogenesis;placenta blood vessel development;cellular response to BMP stimulus;negative regulation of neural precursor cell proliferation
• Cellular component: extracellular region;extracellular space;plasma membrane;membrane;extracellular exosome
• Molecular function: serine-type endopeptidase inhibitor activity