SYT9
protein-codingsynaptotagmin 9, the group of Synaptotagmins
Gene summary
Predicted to enable SNARE binding activity; calcium ion sensor activity; and calcium-dependent phospholipid binding activity. Predicted to be involved in chemical synaptic transmission; regulation of vesicle-mediated transport; and vesicle-mediated transport. Predicted to be located in clathrin-coated endocytic vesicle membrane. Predicted to be active in dense core granule; exocytic vesicle; and plasma membrane. [provided by Alliance of Genome Resources, Jun 2026]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~230.3 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to SYT9 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_175733.4. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 54 | 2 | 56 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 54 | 2 | 0 | 56 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_783860.1 | 7 | MANE Select | |
| Ensembl | ENSP00000324419.6 | 7 | MANE Select | |
| Ensembl | ENSP00000432141.2 | 4 | Standard | |
| Ensembl | ENSP00000434558.1 | 3 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Vesicle-mediated transport
- Membrane Trafficking
- Neuronal System
- Clathrin-mediated endocytosis
- Neurexins and neuroligins
Biological Process
- regulation of dopamine secretion
- vesicle-mediated transport
- calcium ion regulated exocytosis
- regulation of calcium ion-dependent exocytosis
- regulation of insulin secretion
Molecular Function
- SNARE binding
- phosphatidylserine binding
- calcium ion binding
- calcium-dependent phospholipid binding
- phosphatidylinositol-4,5-bisphosphate binding
Cellular Component
- plasma membrane
- cell junction
- integral component of synaptic vesicle membrane
- clathrin-coated vesicle membrane
- secretory granule membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000318881
- Coding exons
- 7
- Length
- 230265
- Individuals with no LoFs
- 125733
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 15
- Defined
- 125748
- p
- 0.0000596
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.32 | 211 | 272 | 0.776 | 0.0000155 | 3216 |
| Missense (PolyPhen) | 77 | 118.84 | 0.64792 | 1414 | ||
| Synonymous | -0.117 | 115 | 113 | 1.01 | 0.00000696 | 956 |
| Loss of Function | 3.29 | 5 | 21.4 | 0.233 | 0.00000128 | 245 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000062 | 0.000062 | rare |
| Latino/Admixed American | 0.000087 | 0.000087 | rare |
| Ashkenazi Jewish | 0.000099 | 0.000099 | rare |
| East Asian | 0.000054 | 0.000054 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000053 | 0.000053 | rare |
| South Asian | 0.000098 | 0.000098 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: May be involved in Ca(2+)-dependent exocytosis of secretory vesicles through Ca(2+) and phospholipid binding to the C2 domain or may serve as Ca(2+) sensors in the process of vesicular trafficking and exocytosis.;
Recessive Scores
- pRec
- 0.120
Intolerance Scores
- LoFtool
- 0.546
- RVIS EVS
- -0.07
- RVIS percentile EVS
- 48.54
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.742
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |