SPINK9

serine peptidase inhibitor Kazal type 9, the group of Serine peptidase inhibitors, Kazal type

Basic information

Region (hg38): 5:148321203-148339852

Links

ENSG00000204909 ∙ NCBI:643394 ∙ OMIM:613511 ∙ HGNC:32951 ∙ Uniprot:Q5DT21 ∙ 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 SPINK9 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SPINK9 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			9
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	0	0

Variants in SPINK9

This is a list of pathogenic ClinVar variants found in the SPINK9 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-148335627-C-G		not specified	Uncertain significance (May 12, 2024)
5-148335631-A-G		not specified	Uncertain significance (Jun 17, 2024)
5-148335647-C-A		not specified	Uncertain significance (Sep 25, 2023)
5-148335651-C-T		not specified	Uncertain significance (Jan 31, 2023)
5-148335663-T-C		not specified	Uncertain significance (Jan 19, 2024)
5-148336422-G-C		not specified	Uncertain significance (Sep 04, 2024)
5-148336431-G-A		not specified	Uncertain significance (Jan 03, 2024)
5-148338551-G-A		not specified	Uncertain significance (Oct 07, 2024)
5-148338553-G-A		not specified	Uncertain significance (Nov 25, 2024)
5-148339680-A-G		not specified	Uncertain significance (Feb 18, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SPINK9	protein_coding	protein_coding	ENST00000377906	4	18647

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0156	0.712	121710	0	22	121732	0.0000904

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.260	40	44.9	0.891	0.00000209	574
Missense in Polyphen		7	11.74	0.59624		165
Synonymous	0.297	13	14.4	0.900	7.83e-7	143
Loss of Function	0.677	3	4.56	0.658	1.92e-7	59

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000129	0.000125
Ashkenazi Jewish	0.00	0.00
East Asian	0.000115	0.000112
Finnish	0.00	0.00
European (Non-Finnish)	0.0000652	0.0000628
Middle Eastern	0.000115	0.000112
South Asian	0.000439	0.000389
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Serine protease inhibitor which specifically inhibits KLK5. May contribute to the regulation of the desquamation process in skin by inhibiting KLK5. {ECO:0000269|PubMed:19190773, ECO:0000269|PubMed:19194479}.
• Pathway: Keratinization;Developmental Biology;Formation of the cornified envelope (Consensus)

Recessive Scores

• pRec: 0.0940

Intolerance Scores

• loftool: 0.694
• rvis_EVS: 0.04
• rvis_percentile_EVS: 56.25

Haploinsufficiency Scores

• pHI: 0.102
• hipred: N
• hipred_score: 0.146
• ghis: 0.456

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.221

Gene Damage Prediction

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

Gene ontology

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