STX17
protein-codingsyntaxin 17, the group of Syntaxins
Gene summary
Enables SNAP receptor activity; SNARE binding activity; and protein phosphatase binding activity. Involved in several processes, including endoplasmic reticulum to Golgi vesicle-mediated transport; endoplasmic reticulum-Golgi intermediate compartment organization; and macroautophagy. Acts upstream of or within protein localization to phagophore assembly site. Located in several cellular components, including endoplasmic reticulum-Golgi intermediate compartment; mitochondria-associated endoplasmic reticulum membrane contact site; and vacuolar membrane. Part of SNARE complex. [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 ~67.9 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 STX17 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_017919.3. 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 | 43 | 43 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 43 | 0 | 0 | 43 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_060389.2 | 7 | MANE Select | |
| Ensembl | ENSP00000259400.6 | 7 | MANE Select | |
| Ensembl | ENSP00000436666.1 | 4 | Standard | |
| Ensembl | ENSP00000433701.1 | 3 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Autophagy - animal - Homo sapiens (human)
- SNARE interactions in vesicular transport - Homo sapiens (human)
- Nicotine Pathway (Dopaminergic Neuron), Pharmacodynamics
- Vesicle-mediated transport
- Membrane Trafficking
Biological Process
- intracellular protein transport
- endoplasmic reticulum to Golgi vesicle-mediated transport
- vesicle fusion
- Golgi organization
- autophagosome membrane docking
Molecular Function
- SNARE binding
- SNAP receptor activity
- protein binding
- protein kinase binding
- protein phosphatase binding
Cellular Component
- autophagosome membrane
- mitochondrion
- lysosomal membrane
- autophagosome
- endoplasmic reticulum membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000259400
- Coding exons
- 7
- Length
- 63704
- Individuals with no LoFs
- 125714
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 33
- Defined
- 125747
- p
- 0.000131
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.594 | 136 | 157 | 0.867 | 0.00000765 | 1976 |
| Missense (PolyPhen) | 26 | 38.625 | 0.67314 | 470 | ||
| Synonymous | 0.813 | 45 | 52.5 | 0.857 | 0.00000241 | 574 |
| Loss of Function | 1.73 | 9 | 16.6 | 0.542 | 9.59e-7 | 191 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00012 | 0.00012 | rare |
| Latino/Admixed American | 0.00041 | 0.00040 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0.000046 | 0.000046 | rare |
| European (Non-Finnish) | 0.00012 | 0.00011 | rare |
| South Asian | 0.000066 | 0.000065 | rare |
| Other | 0.00016 | 0.00016 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: SNAREs, soluble N-ethylmaleimide-sensitive factor- attachment protein receptors, are essential proteins for fusion of cellular membranes. SNAREs localized on opposing membranes assemble to form a trans-SNARE complex, an extended, parallel four alpha-helical bundle that drives membrane fusion. STX17 is a SNARE of the autophagosome involved in autophagy through the direct control of autophagosome membrane fusion with the lysosome membrane (PubMed:23217709, PubMed:25686604). May also play a role in the early secretory pathway where it may maintain the architecture of the endoplasmic reticulum-Golgi intermediate compartment/ERGIC and Golgi and/or regulate transport between the endoplasmic reticulum, the ERGIC and the Golgi (PubMed:21545355). {ECO:0000269|PubMed:21545355, ECO:0000269|PubMed:23217709, ECO:0000269|PubMed:25686604}.;
Recessive Scores
- pRec
- 0.119
Intolerance Scores
- LoFtool
- 0.473
- RVIS EVS
- 0.15
- RVIS percentile EVS
- 64.32
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.801
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |