STX19
protein-codingsyntaxin 19, the group of Syntaxins
Gene summary
Predicted to enable SNAP receptor activity and SNARE binding activity. Predicted to be involved in intracellular protein transport; synaptic vesicle fusion to presynaptic active zone membrane; and vesicle docking. Predicted to be located in cytoplasm and membrane. Predicted to be part of SNARE complex. Predicted to be active in endomembrane system and presynaptic active zone membrane. [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 ~14.2 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 STX19 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001001850.3. 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 | 35 | 2 | 37 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 35 | 2 | 0 | 37 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001001850.1 | 1 | MANE Select | |
| Ensembl | ENSP00000320679.2 | 1 | MANE Select | |
| Ensembl | ENSP00000526606.1 | 1 | Standard | |
| Ensembl | ENSP00000526606.1 | 1 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- SNARE interactions in vesicular transport - Homo sapiens (human)
- Nicotine Pathway (Dopaminergic Neuron), Pharmacodynamics
Biological Process
- intracellular protein transport
- exocytosis
- vesicle fusion
- synaptic vesicle fusion to presynaptic active zone membrane
- vesicle docking
Molecular Function
- SNARE binding
- SNAP receptor activity
- protein binding
Cellular Component
- plasma membrane
- synaptic vesicle
- endomembrane system
- integral component of membrane
- SNARE complex
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000315099
- Coding exons
- 1
- Length
- 14242
- Individuals with no LoFs
- 125627
- Homozygous LoFs
- 1
- Heterozygous LoFs
- 65
- Defined
- 125693
- p
- 0.000263
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.464 | 159 | 143 | 1.11 | 0.00000648 | 1961 |
| Missense (PolyPhen) | 46 | 44.538 | 1.0328 | 627 | ||
| Synonymous | -1.08 | 56 | 46.6 | 1.20 | 0.00000200 | 515 |
| Loss of Function | -0.0505 | 10 | 9.83 | 1.02 | 4.89e-7 | 130 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00037 | 0.00037 | rare |
| Latino/Admixed American | 0.00055 | 0.00055 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.000054 | 0.000054 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.00017 | 0.00017 | rare |
| South Asian | 0.00066 | 0.00062 | rare |
| Other | 0.00033 | 0.00033 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Plays a role in endosomal trafficking of the epidermal growth factor receptor (EGFR). {ECO:0000250|UniProtKB:Q8R1Q0}.;
Intolerance Scores
- LoFtool
- 0.837
- RVIS EVS
- 0.26
- RVIS percentile EVS
- 70.06
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.114
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |