SPINK4

serine peptidase inhibitor Kazal type 4, the group of Serine peptidase inhibitors, Kazal type

Basic information

Region (hg38): 9:33218365-33248567

Links

ENSG00000122711 ∙ NCBI:27290 ∙ OMIM:613929 ∙ HGNC:16646 ∙ Uniprot:O60575 ∙ 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 SPINK4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SPINK4 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			12	1		13
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	12	1	0

Variants in SPINK4

This is a list of pathogenic ClinVar variants found in the SPINK4 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-33240233-G-A		not specified	Likely benign (Sep 29, 2023)
9-33245130-G-A		not specified	Uncertain significance (Apr 11, 2023)
9-33246620-T-G		not specified	Uncertain significance (Jul 25, 2023)
9-33246646-A-G		not specified	Uncertain significance (Nov 18, 2022)
9-33246647-C-A		not specified	Uncertain significance (Aug 13, 2021)
9-33246670-G-C		not specified	Uncertain significance (Feb 06, 2023)
9-33246674-G-A		not specified	Uncertain significance (Jan 22, 2024)
9-33246676-G-C		not specified	Uncertain significance (Jan 29, 2024)
9-33246694-T-C		not specified	Uncertain significance (Dec 09, 2023)
9-33246698-C-T		not specified	Uncertain significance (Jun 29, 2022)
9-33246712-C-T		not specified	Uncertain significance (Mar 07, 2024)
9-33246725-G-A		not specified	Uncertain significance (Apr 07, 2023)
9-33248439-G-C		not specified	Uncertain significance (Nov 08, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SPINK4	protein_coding	protein_coding	ENST00000379721	4	30203

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.296	0.631	125743	0	5	125748	0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.342	41	47.6	0.861	0.00000249	552
Missense in Polyphen		19	15.753	1.2061		191
Synonymous	0.842	14	18.6	0.752	0.00000106	166
Loss of Function	1.37	1	3.94	0.254	1.66e-7	50

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000213	0.000185
Ashkenazi Jewish	0.0000996	0.0000992
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000879	0.00000879
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.706
• rvis_EVS: 0.61
• rvis_percentile_EVS: 83.07

Haploinsufficiency Scores

• pHI: 0.107
• hipred: N
• hipred_score: 0.172

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: Spink4

Gene ontology

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