SYT7

Chr 11

synaptotagmin 7

Also known as: IPCA-7, IPCA7, PCANAP7, SYT-VII, SYTVII

NCBI Gene: 9066ENSG00000011347UniProt: O43581

This gene is a member of the synaptotagmin gene family and encodes a protein similar to other family members that mediate calcium-dependent regulation of membrane trafficking in synaptic transmission. A similar protein in rodents mediates hormone secretion and lysosome exocytosis. In humans, expression of this gene has been associated with prostate cancer. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Oct 2011]

59
ClinVar variants
11
Pathogenic / LP
0.96
pLI score· haploinsufficient
0
Active trials
Clinical Summary— SYT7
⚡
Population Constraint (gnomAD)
Highly constrained gene — heterozygous loss-of-function variants are very rare in the population (pLI 0.96). One damaged copy is likely sufficient to cause disease.
📋
ClinVar Variants
11 Pathogenic / Likely Pathogenic· 44 VUS of 59 total submissions
Some data sources returned errors (1)

omim: Error: OMIM fetch failed: 429

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
LoF intolerant — likely haploinsufficient
LoF Constraint?LOEUF (Loss-of-function Observed/Expected Upper bound Fraction) is the upper bound of the 90% CI for LoF OE — the preferred gnomAD v4 metric. Lower = more intolerant to LoF. LOEUF < 0.35 = highly constrained.
0.33LOEUF
pLI 0.963
Z-score 3.63
OE 0.10 (0.04–0.33)
Highly constrained

Highly LoF-intolerant (top ~10% of genes)

Missense Constraint?Missense Z-score: standard deviations fewer missense variants observed vs. expected. Z > 3.09 (p < 0.001) = gene does not tolerate missense variation. OE missense < 0.6 is also considered constrained.
2.21Z-score
OE missense 0.64 (0.57–0.72)
189 obs / 296.0 exp
Mild constraint

Moderately missense-constrained (top ~2.5%)

Observed / Expected Ratios?Shaded band = 90% confidence interval. Vertical tick = point estimate. Grey threshold line = gnomAD constraint cutoff for that variant class.
LoF OE?Ratio of observed to expected LoF variants. Upper CI bound (LOEUF) ≤ 0.35 = strong LoF constraint signal.0.10 (0.04–0.33)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.0.64 (0.57–0.72)
0≤0.61.4
Synonymous OE?Control metric — synonymous variants are largely neutral and expected near OE = 1.0. Significant deviation may indicate annotation issues.0.98
0≤1.21.6
LoF obs/exp: 2 / 19.1Missense obs/exp: 189 / 296.0Syn Z: 0.17

ClinVar Variant Classifications

59 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic7
Likely Pathogenic4
VUS44
Likely Benign3
Benign1
7
Pathogenic
4
Likely Pathogenic
44
VUS
3
Likely Benign
1
Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
7
0
7
Likely Pathogenic
0
0
4
0
4
VUS
0
40
4
0
44
Likely Benign
0
1
1
1
3
Benign
0
1
0
0
1
Total04216159

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

Protein Context — Lollipop Plot

SYT7 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

OMIM — Genotype-Phenotype

OMIM

No OMIM entries found.

Clinical Literature
Landmark / reviewRecent case evidence
Key Publications
Landmark & review papers · by relevance
PubMed
SYT7 acts as a driver of hepatic metastasis formation of gastric cancer cells.
Kanda M et al.·Oncogene
2018
High SYT7 expression is associated with poor prognosis in human non-small cell lung carcinoma.
Han Q et al.·Pathol Res Pract
2020
Synaptotagmin-7 deficiency induces mania-like behavioral abnormalities through attenuating GluN2B activity.
Wang QW et al.·Proc Natl Acad Sci U S A
2020
SYT7 as a Potential Prognostic Marker Promotes the Metastasis of Epithelial Ovarian Cancer Cells by Activating the STAT3 Pathway.
Li Y et al.·Mol Carcinog
2024
Synaptotagmin-7 is a key factor for bipolar-like behavioral abnormalities in mice.
Shen W et al.·Proc Natl Acad Sci U S A
2020
Exploration of key factors in Gingival Crevicular fluids from patients undergoing Periodontally Accelerated Osteogenic Orthodontics (PAOO) using proteome analysis.
Wu J et al.·BMC Oral Health
2023Cohort
Effects of protein-coding variants on blood metabolite measurements and clinical biomarkers in the UK Biobank.
Nag A et al.·Am J Hum Genet
2023
Stimulation of MMP-1 and CCL2 by NAMPT in PDL cells.
Nokhbehsaim M et al.·Mediators Inflamm
2013
Cross-regulation of defective endolysosome trafficking and enhanced autophagy through TFEB in UNC13D deficiency.
Zhang J et al.·Autophagy
2019
MACE-Seq-based coding RNA and TrueQuant-based small RNA profile in breast cancer: tumor-suppressive miRNA-1275 identified as a novel marker.
Majed SO et al.·BMC Cancer
2021
Top 10 resultsSearch PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →

External Resources

Links to major genomics databases and tools