SYT10

Chr 12

synaptotagmin 10

NCBI Gene: 341359 ENSG00000110975 UniProt: Q6XYQ8

SYT10 encodes a calcium sensor protein that specifically regulates calcium-dependent exocytosis of IGF1-containing secretory vesicles in olfactory bulb neurons, which is required for normal smell perception. The gene is not highly constrained against loss-of-function variants (pLI = 0.00006), and no established human disease phenotypes have been reported for SYT10 mutations to date.

ResearchSummary from RefSeq, UniProt

Predicted to enable several functions, including calcium ion binding activity; calcium ion sensor activity; and calcium-dependent phospholipid binding activity. Predicted to be involved in positive regulation of calcium ion-dependent exocytosis; presynaptic dense core vesicle exocytosis; and sensory perception of smell. Predicted to be located in transport vesicle membrane. Predicted to be active in exocytic vesicle and plasma membrane. [provided by Alliance of Genome Resources, Jun 2026]

ResearchGenerating clinical summary…

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

0.75

LOEUF

Multiple*

Mechanism· predicted

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

0.75LOEUF

pLI 0.000

Z-score 2.48

OE 0.45 (0.28–0.75)

Tolerant

Typical tolerance to LoF variation

Missense Constraint?

0.45Z-score

OE missense 0.92 (0.84–1.02)

265 obs / 286.5 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.45 (0.28–0.75)

0≤0.351.4

Missense OE?0.92 (0.84–1.02)

0≤0.61.4

Synonymous OE?0.95

0≤1.21.6

LoF obs/exp: 11 / 24.2Missense obs/exp: 265 / 286.5Syn Z: 0.37

Background carrier burden — how many people carry a rare variant somewhere in SYT10?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 110

650 rare PASS variants

Rare truncating (LoF)

1 in 1,800

95 rare PASS variants

Rare synonymous (reference)

1 in 140

252 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for SYT10. 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 160	1 in 1,900
South Asian	~43k	1 in 83	1 in 950
Remaining (unassigned)	~30k	1 in 69	1 in 2,200
European (Finnish)	~27k	1 in 470	1 in 1,300
Admixed American	~22k	1 in 78	≈ 1 in 4,500
African / African American	~21k	1 in 110	≈ 1 in 9,300
East Asian	~20k	1 in 110	1 in 900
Ashkenazi Jewish	~13k	1 in 410	≈ 1 in 6,500
Middle Eastern	~2,884	1 in 110	≈ 1 in 1,400

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): All 7 coding exons well covered in gnomAD exomes and genomes.? see exons ↓