SPINK6

serine peptidase inhibitor Kazal type 6, the group of Serine peptidase inhibitors, Kazal type

Basic information

Region (hg38): 5:148202794-148215137

Links

ENSG00000178172 ∙ NCBI:404203 ∙ OMIM:615868 ∙ HGNC:29486 ∙ Uniprot:Q6UWN8 ∙ 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 SPINK6 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SPINK6 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			6			6
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	6	0	0

Variants in SPINK6

This is a list of pathogenic ClinVar variants found in the SPINK6 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-148213920-G-A		not specified	Uncertain significance (May 25, 2022)
5-148213937-A-C		not specified	Uncertain significance (Dec 05, 2022)
5-148213967-C-T		not specified	Uncertain significance (Feb 24, 2025)
5-148213988-A-G		not specified	Uncertain significance (Dec 15, 2022)
5-148213989-C-T		not specified	Uncertain significance (Apr 08, 2022)
5-148214024-G-T		not specified	Uncertain significance (Mar 04, 2024)
5-148214906-A-G		not specified	Uncertain significance (Mar 21, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SPINK6	protein_coding	protein_coding	ENST00000325630	4	12344

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.53e-7	0.0576	125721	0	21	125742	0.0000835

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.376	48	41.2	1.17	0.00000190	516
Missense in Polyphen		21	18.456	1.1378		220
Synonymous	0.658	11	14.1	0.778	6.10e-7	142
Loss of Function	-1.39	8	4.73	1.69	1.99e-7	60

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000116	0.000116
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000796	0.0000791
Middle Eastern	0.00	0.00
South Asian	0.000269	0.000261
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Serine protease inhibitor selective for kallikreins. Efficiently inhibits KLK4, KLK5, KLK6, KLK7, KLK12, KLK13 and KLK14. Doesn't inhibit KLK8. {ECO:0000269|PubMed:20667819, ECO:0000269|PubMed:21439340}.
• Pathway: Keratinization;Developmental Biology;Formation of the cornified envelope (Consensus)

Intolerance Scores

• loftool: 0.750
• rvis_EVS: 0.52
• rvis_percentile_EVS: 80.46

Haploinsufficiency Scores

• pHI: 0.258
• hipred: N
• hipred_score: 0.144

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0861

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Spink6

Gene ontology

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