SPINT4

serine peptidase inhibitor, Kunitz type 4

Basic information

Region (hg38): 20:45722346-45725830

Previous symbols: [ "C20orf137" ]

Links

ENSG00000149651 ∙ NCBI:391253 ∙ OMIM:619430 ∙ HGNC:16130 ∙ Uniprot:Q6UDR6 ∙ 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 SPINT4 gene.

• Inborn genetic diseases (5 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SPINT4 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			5			5
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	5	0	0

Variants in SPINT4

This is a list of pathogenic ClinVar variants found in the SPINT4 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-45723897-A-G		not specified	Uncertain significance (Mar 08, 2024)
20-45723925-A-C		not specified	Uncertain significance (Aug 14, 2023)
20-45723995-C-A		not specified	Uncertain significance (Feb 22, 2023)
20-45723995-C-G		not specified	Uncertain significance (Dec 01, 2022)
20-45724023-C-T		not specified	Likely benign (Jan 24, 2024)
20-45724026-G-A		not specified	Uncertain significance (Jun 30, 2022)
20-45724026-G-C		not specified	Likely benign (Feb 05, 2024)
20-45724033-C-G		not specified	Uncertain significance (Apr 08, 2022)
20-45724054-C-T		not specified	Uncertain significance (Sep 23, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SPINT4	protein_coding	protein_coding	ENST00000279058	3	3480

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0844	0.771	120591	0	12	120603	0.0000498

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.334	44	50.7	0.868	0.00000252	651
Missense in Polyphen		11	13.161	0.8358		177
Synonymous	-0.241	20	18.7	1.07	9.41e-7	169
Loss of Function	1.08	2	4.45	0.449	2.83e-7	59

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.000229	0.000230
Finnish	0.00	0.00
European (Non-Finnish)	0.0000721	0.0000721
Middle Eastern	0.000229	0.000230
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0701

Intolerance Scores

• loftool: 0.727
• rvis_EVS: 0.46
• rvis_percentile_EVS: 78.16

Haploinsufficiency Scores

• pHI: 0.0603
• hipred: N
• hipred_score: 0.180

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.319

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Spint4

Gene ontology

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