SPINK13

serine peptidase inhibitor Kazal type 13, the group of Serine peptidase inhibitors, Kazal type

Basic information

Region (hg38): 5:148268180-148286255

Links

ENSG00000214510 ∙ NCBI:153218 ∙ OMIM:615205 ∙ HGNC:27200 ∙ Uniprot:Q1W4C9 ∙ 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 SPINK13 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SPINK13 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			7	2		9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1	1		2
Total	0	0	8	3	0

Variants in SPINK13

This is a list of pathogenic ClinVar variants found in the SPINK13 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-148270098-T-C		not specified	Uncertain significance (Oct 08, 2024)
5-148270100-T-A		not specified	Uncertain significance (Aug 10, 2024)
5-148270124-A-G		not specified	Likely benign (Sep 17, 2021)
5-148274352-T-C		not specified	Uncertain significance (Dec 13, 2022)
5-148274357-T-A		not specified	Likely benign (Sep 30, 2021)
5-148274358-A-G		not specified	Uncertain significance (Jan 18, 2025)
5-148274361-C-T		not specified	Uncertain significance (Dec 06, 2021)
5-148274362-G-A		not specified	Likely benign (May 04, 2022)
5-148274364-G-T		not specified	Uncertain significance (Jun 07, 2024)
5-148282120-A-T		not specified	Uncertain significance (Dec 27, 2023)
5-148282168-C-T		not specified	Uncertain significance (Oct 27, 2022)
5-148282200-C-G		not specified	Uncertain significance (Mar 01, 2025)
5-148282212-T-G		not specified	Uncertain significance (Jun 30, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SPINK13	protein_coding	protein_coding	ENST00000512953	4	18075

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000476	0.451	124768	0	4	124772	0.0000160

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.216	55	50.7	1.09	0.00000252	624
Missense in Polyphen		15	12.364	1.2132		163
Synonymous	1.13	10	15.7	0.636	6.77e-7	157
Loss of Function	0.110	5	5.27	0.948	3.09e-7	55

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000870	0.0000870
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000884	0.00000883
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be a serine protease inhibitor (By similarity). Essential for sperm maturation and fertility. Inhibits sperm acrosome reaction, protecting sperm from premature reaction (By similarity). {ECO:0000250}.
• Pathway: Glucocorticoid Receptor Pathway;Nuclear Receptors Meta-Pathway (Consensus)

Intolerance Scores

• rvis_EVS: -0.01
• rvis_percentile_EVS: 52.85

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.123
• ghis: 0.476

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Spink13

Gene ontology

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