SYT17
protein-codingsynaptotagmin 17, the group of Synaptotagmins
Gene summary
Predicted to enable SNARE binding activity; calcium ion sensor activity; and calcium-dependent phospholipid binding activity. Involved in positive regulation of dendrite extension and regulation of postsynaptic neurotransmitter receptor internalization. Is active in glutamatergic synapse and postsynapse. [provided by Alliance of Genome Resources, Jul 2025]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~100.4 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 SYT17 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_016524.4. 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 | 4 | 1 | 5 | |||
| missense | 65 | 65 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 0 | 0 | 70 | 1 | 0 | 71 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_057608.2 | 8 | MANE Select | |
| Ensembl | ENSP00000347538.2 | 8 | MANE Select | |
| RefSeq | NP_001295086.1 | 8 | Standard | |
| RefSeq | NP_001317438.1 | 5 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- regulation of dopamine secretion
- synaptic vesicle exocytosis
- vesicle-mediated transport
- calcium ion regulated exocytosis
- regulation of calcium ion-dependent exocytosis
Molecular Function
- SNARE binding
- phosphatidylserine binding
- calcium ion binding
- protein binding
- calcium-dependent phospholipid binding
Cellular Component
- trans-Golgi network
- plasma membrane
- exocytic vesicle
- presynapse
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000355377
- Coding exons
- 8
- Length
- 100360
- Individuals with no LoFs
- 125721
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 27
- Defined
- 125748
- p
- 0.000107
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.18 | 231 | 287 | 0.804 | 0.0000189 | 3106 |
| Missense (PolyPhen) | 57 | 80.605 | 0.70715 | 943 | ||
| Synonymous | 0.243 | 118 | 121 | 0.972 | 0.00000859 | 945 |
| Loss of Function | 1.81 | 11 | 19.7 | 0.559 | 9.06e-7 | 238 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00018 | 0.00018 | rare |
| Latino/Admixed American | 0.00012 | 0.00012 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00027 | 0.00027 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.00011 | 0.00011 | rare |
| South Asian | 0.000098 | 0.000098 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Plays a role in dendrite formation by melanocytes (PubMed:23999003). {ECO:0000269|PubMed:23999003}.;
Recessive Scores
- pRec
- 0.131
Intolerance Scores
- LoFtool
- 0.620
- RVIS EVS
- -1.27
- RVIS percentile EVS
- 5.24
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.741
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |