STX2
protein-codingsyntaxin 2, the group of Syntaxins
Gene summary
The product of this gene belongs to the syntaxin/epimorphin family of proteins. The syntaxins are a large protein family implicated in the targeting and fusion of intracellular transport vesicles. The product of this gene regulates epithelial-mesenchymal interactions and epithelial cell morphogenesis and activation. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jul 2008]
- STX2B
- STX2C
- STX2A
- EPIM
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~49.7 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AR
Disease ID:MONDO:0004983
Submitter: Ambry Genetics
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to STX2 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_194356.4. 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 | 1 | 1 | ||||
| missense | 44 | 1 | 1 | 46 | ||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 0 | 0 | 46 | 1 | 1 | 48 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_919337.1 | 10 | MANE Select | |
| Ensembl | ENSP00000376178.2 | 10 | MANE Select | |
| RefSeq | NP_001337978.2 | 10 | Standard | |
| RefSeq | NP_001337979.1 | 9 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Synaptic vesicle cycle - Homo sapiens (human)
- SNARE interactions in vesicular transport - Homo sapiens (human)
- Nicotine Pathway (Dopaminergic Neuron), Pharmacodynamics
- Synaptic Vesicle Pathway
- Splicing factor NOVA regulated synaptic proteins
Biological Process
- intracellular protein transport
- exocytosis
- vesicle fusion
- signal transduction
- acrosome reaction
Molecular Function
- SNARE binding
- SNAP receptor activity
- protein binding
- protein dimerization activity
- calcium-dependent protein binding
Cellular Component
- extracellular space
- plasma membrane
- synaptic vesicle
- endomembrane system
- integral component of membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000392373
- Coding exons
- 10
- Length
- 49667
- Individuals with no LoFs
- 125715
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 33
- Defined
- 125748
- p
- 0.000131
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.108 | 160 | 164 | 0.976 | 0.00000928 | 1913 |
| Missense (PolyPhen) | 52 | 54.525 | 0.95369 | 650 | ||
| Synonymous | 0.173 | 52 | 53.6 | 0.970 | 0.00000313 | 505 |
| Loss of Function | 1.22 | 13 | 18.7 | 0.695 | 0.00000114 | 215 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00019 | 0.00018 | rare |
| Latino/Admixed American | 0.00012 | 0.00012 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00028 | 0.00027 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.00015 | 0.00015 | rare |
| South Asian | 0.00014 | 0.00013 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Essential for epithelial morphogenesis. May mediate Ca(2+)-regulation of exocytosis acrosomal reaction in sperm.;
Recessive Scores
- pRec
- 0.234
Intolerance Scores
- LoFtool
- 0.941
- RVIS EVS
- 0.57
- RVIS percentile EVS
- 82.08
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.784
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |