SPINK13

Chr 5

serine peptidase inhibitor Kazal type 13

Also known as: HBVDNAPTP1, HESPINTOR, LiESP6, SPINK5L3

NCBI Gene: 153218 ENSG00000214510 UniProt: Q1W4C9 OMIM: 615205

Predicted to enable serine-type endopeptidase inhibitor activity. Predicted to be involved in negative regulation of acrosome reaction. Predicted to be located in extracellular region. [provided by Alliance of Genome Resources, Jul 2025]

OMIM Research

OMIM ResearchGenerating clinical summary…

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

1.77

LOEUF

Multiple*

Mechanism· predicted

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

1.77LOEUF

pLI 0.000

Z-score 0.11

OE 0.95 (0.49–1.77)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

-0.22Z-score

OE missense 1.09 (0.87–1.36)

55 obs / 50.7 exp

Tolerant

Tolerant to missense variation

Observed / Expected Ratios?

LoF OE?0.95 (0.49–1.77)

0≤0.351.4

Missense OE?1.09 (0.87–1.36)

0≤0.61.4

Synonymous OE?0.64

0≤1.21.6

LoF obs/exp: 5 / 5.3Missense obs/exp: 55 / 50.7Syn Z: 1.13

Background carrier burden — how many people carry a rare variant somewhere in SPINK13?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 530

120 rare PASS variants

Rare truncating (LoF)

1 in 1,000

30 rare PASS variants

Rare synonymous (reference)

1 in 1,200

33 rare PASS variants

Rare missense and truncating variants are carried at similar rates in SPINK13; this gene does not show strong loss-of-function constraint by this measure. A background rate for each class, not the frequency of any particular variant; thin-coverage exons undercount.

By genetic ancestry · 9 gnomAD groups · rare = under 0.1% in that group

Group	People	Missense	Truncating
European (non-Finnish)	~556k	1 in 390	1 in 1,900
South Asian	~43k	1 in 300	1 in 1,600
Remaining (unassigned)	~30k	1 in 210	1 in 1,100
European (Finnish)	~27k	1 in 1,900	none seen
Admixed American	~22k	1 in 320	1 in 4,500
African / African American	~21k	1 in 240	1 in 930
East Asian	~20k	1 in 1,100	none seen
Ashkenazi Jewish	~13k	1 in 230	≈ 1 in 6,200
Middle Eastern	~2,884	1 in 260	1 in 260

Each group is summed over the variants that are rare in that group. Grey ≈ figures rest on fewer than five expected carriers — too few to distinguish groups. Differences mostly reflect how many people were sampled and how much variation each ancestry carries, not disease risk.

Exome coverage (gnomAD): 3 of 4 coding exons well covered in gnomAD exomes; exon 5 marginal. Genomes: all 4.? see exons ↓