SPINK7

serine peptidase inhibitor Kazal type 7, the group of Serine peptidase inhibitors, Kazal type

Basic information

Region (hg38): 5:148312419-148315922

Links

ENSG00000145879 ∙ NCBI:84651 ∙ OMIM:617288 ∙ HGNC:24643 ∙ Uniprot:P58062 ∙ 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 SPINK7 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SPINK7 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			9	1		10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	9	1	0

Variants in SPINK7

This is a list of pathogenic ClinVar variants found in the SPINK7 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-148312502-C-A		not specified	Uncertain significance (Feb 23, 2023)
5-148312508-C-G		not specified	Uncertain significance (Feb 06, 2023)
5-148313389-C-A		not specified	Uncertain significance (Jun 02, 2023)
5-148314109-A-G		not specified	Uncertain significance (Feb 23, 2023)
5-148314140-T-C		not specified	Uncertain significance (Jun 21, 2023)
5-148314173-G-C		not specified	Uncertain significance (Jun 26, 2024)
5-148314206-A-G		not specified	Uncertain significance (Oct 07, 2024)
5-148314217-G-A		not specified	Uncertain significance (Jul 02, 2024)
5-148314218-A-T		not specified	Uncertain significance (Jul 02, 2024)
5-148315655-G-A		not specified	Likely benign (Oct 18, 2021)
5-148315658-C-G		not specified	Uncertain significance (Feb 13, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SPINK7	protein_coding	protein_coding	ENST00000274565	4	3504

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0784	0.764	125674	0	21	125695	0.0000835

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0439	45	44.2	1.02	0.00000200	551
Missense in Polyphen		22	19.093	1.1523		229
Synonymous	-0.804	21	16.8	1.25	9.07e-7	155
Loss of Function	1.02	2	4.28	0.467	1.79e-7	61

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000735	0.000735
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000176	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.000198	0.000196
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probable serine protease inhibitor.

Recessive Scores

• pRec: 0.0993

Intolerance Scores

• loftool: 0.712
• rvis_EVS: 0.21
• rvis_percentile_EVS: 67.72

Haploinsufficiency Scores

• pHI: 0.134
• hipred: N
• hipred_score: 0.344
• ghis: 0.378

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.683

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Spink7

Gene ontology

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