SPINT2

serine peptidase inhibitor, Kunitz type 2

Basic information

Region (hg38): 19:38244034-38292615

Links

ENSG00000167642 ∙ NCBI:10653 ∙ OMIM:605124 ∙ HGNC:11247 ∙ Uniprot:O43291 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• congenital secretory sodium diarrhea 3 (Strong), mode of inheritance: AR
• congenital secretory sodium diarrhea 3 (Moderate), mode of inheritance: AR
• congenital secretory sodium diarrhea 3 (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Diarrhea 3, secretory sodium, congenital, with or without other congenital anomalies	AD	Gastrointestinal	Due to fecal sodium loss, individuals may present with severe (potentially lethal) secretory diarrhea and related electrolyte/metabolic derangements, including hyponatremic metabolic acidosis, and recognition may allow appropriate medical management, which includes parenteral nutrition (weaning from parenteral nutrition, with oral sodium citrate supplementation, is possible in childhood	Craniofacial; Dermatologic; Gastrointestinal; Hematologic; Musculoskeletal; Ophthalmologic	11113072; 17786112; 19185281; 20009592

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SPINT2 gene.

• not provided (119 variants)
• Inborn genetic diseases (8 variants)
• Congenital secretory sodium diarrhea 3 (5 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SPINT2 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				29	3	32
missense	1	2	40	4	3	50
nonsense						0
start loss	1					1
frameshift		1				1
inframe indel						0
splice donor/acceptor (+/-2bp)		3				3
splice region			4	4	2	10
non coding				23	5	28
Total	2	6	40	56	11

Highest pathogenic variant AF is 0.000138

Variants in SPINT2

This is a list of pathogenic ClinVar variants found in the SPINT2 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-38251334-C-T		not specified	Uncertain significance (Jul 21, 2021)
19-38251340-C-G		not specified	Uncertain significance (Dec 07, 2023)
19-38251340-C-T		not specified	Uncertain significance (Jan 23, 2023)
19-38251347-G-T		not specified	Uncertain significance (Sep 22, 2022)
19-38251350-G-C		not specified	Uncertain significance (Jun 02, 2023)
19-38251388-C-A		not specified	Uncertain significance (Jan 20, 2023)
19-38251388-C-T		not specified	Uncertain significance (Dec 02, 2022)
19-38252315-T-A		not specified	Likely benign (Feb 05, 2024)
19-38252904-C-T		not specified	Uncertain significance (Aug 30, 2022)
19-38252905-G-A		not specified	Uncertain significance (Jul 21, 2021)
19-38256231-C-T		not specified	Uncertain significance (May 04, 2023)
19-38256312-C-A		not specified	Uncertain significance (Feb 10, 2022)
19-38256312-C-G		not specified	Uncertain significance (Oct 04, 2022)
19-38256321-C-T		not specified	Uncertain significance (Dec 06, 2021)
19-38264308-G-A			Benign (Jun 19, 2021)
19-38264348-G-A			Benign (Jun 19, 2021)
19-38264452-C-G			Benign (Jun 19, 2021)
19-38264766-C-G			Benign (Jun 19, 2021)
19-38264893-A-T		Congenital secretory sodium diarrhea 3	Pathogenic (Feb 01, 2009)
19-38264895-G-A			Pathogenic (Oct 24, 2022)
19-38264897-C-T			Uncertain significance (Jul 10, 2023)
19-38264932-C-T			Uncertain significance (Nov 04, 2020)
19-38264937-C-T			Likely benign (Nov 24, 2023)
19-38264938-C-T			Benign (Jan 06, 2024)
19-38264967-C-A			Likely benign (Sep 30, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SPINT2	protein_coding	protein_coding	ENST00000301244	7	48580

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000751	0.931	125726	0	22	125748	0.0000875

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.997	118	153	0.773	0.00000960	1631
Missense in Polyphen		25	36.717	0.68088		436
Synonymous	0.477	60	64.9	0.925	0.00000400	517
Loss of Function	1.61	7	13.4	0.523	6.84e-7	145

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000905	0.0000905
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.000149	0.000149
Middle Eastern	0.000109	0.000109
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Inhibitor of HGF activator. Also inhibits plasmin, plasma and tissue kallikrein, and factor XIa.
• Disease: DISEASE: Diarrhea 3, secretory sodium, congenital, with or without other congenital anomalies (DIAR3) [MIM:270420]: A disease characterized by life-threatening secretory diarrhea, severe metabolic acidosis and hyponatremia. Hyponatremia is secondary to extraordinarily high fecal sodium loss, with low or normal excretion of urinary sodium, in the absence of infectious, autoimmune and endocrine causes. {ECO:0000269|PubMed:19185281}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: Signal Transduction;MET Receptor Activation;Signaling by MET;Signaling by MST1;Signaling by Receptor Tyrosine Kinases (Consensus)

Recessive Scores

• pRec: 0.335

Intolerance Scores

• loftool: 0.664
• rvis_EVS: 0.44
• rvis_percentile_EVS: 77.7

Haploinsufficiency Scores

• pHI: 0.100
• hipred: N
• hipred_score: 0.210
• ghis: 0.406

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.539

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Spint2
• 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); embryo 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)

Gene ontology

• Biological process: neural tube closure;establishment or maintenance of cell polarity;negative regulation of endopeptidase activity;negative regulation of cell-cell adhesion;epithelial cell morphogenesis involved in placental branching;basement membrane organization;cellular response to BMP stimulus;negative regulation of cell motility;negative regulation of neural precursor cell proliferation
• Cellular component: extracellular region;cytoplasm;plasma membrane;integral component of membrane
• Molecular function: endopeptidase inhibitor activity;serine-type endopeptidase inhibitor activity