STX10
protein-codingsyntaxin 10, the group of Syntaxins
Gene summary
This gene belongs to the syntaxin family and encodes a soluble N-ethylmaleimide sensitive factor attachment protein receptor (SNARE). The encoded protein is involved in docking and fusion events at the Golgi apparatus. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2012]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~6.3 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 STX10 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_003765.3. 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 | 1 | 1 | ||||
| missense | 44 | 1 | 45 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 3 | 3 | ||||
| Total | 0 | 0 | 48 | 1 | 0 | 49 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_003756.1 | 8 | MANE Select | |
| Ensembl | ENSP00000466298.1 | 8 | MANE Select | |
| RefSeq | NP_001258538.1 | 7 | Standard | |
| RefSeq | NP_001258539.1 | 7 | 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
- Vesicle-mediated transport
- Membrane Trafficking
- Retrograde transport at the Trans-Golgi-Network
Biological Process
- intracellular protein transport
- vesicle fusion
- regulation of protein localization
- early endosome to Golgi transport
- retrograde transport, endosome to Golgi
Molecular Function
- SNARE binding
- SNAP receptor activity
- protein binding
- syntaxin binding
Cellular Component
- trans-Golgi network
- cytosol
- synaptic vesicle
- endomembrane system
- integral component of membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000587230
- Coding exons
- 8
- Length
- 6326
- Individuals with no LoFs
- 125682
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 66
- Defined
- 125748
- p
- 0.000262
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.00708 | 159 | 159 | 1.00 | 0.00000916 | 1620 |
| Missense (PolyPhen) | 41 | 35.368 | 1.1592 | 432 | ||
| Synonymous | 0.143 | 64 | 65.5 | 0.978 | 0.00000410 | 472 |
| Loss of Function | 0.141 | 14 | 14.6 | 0.960 | 6.72e-7 | 146 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00069 | 0.00068 | rare |
| Latino/Admixed American | 0.00035 | 0.00035 | rare |
| Ashkenazi Jewish | 0.00010 | 0.000099 | rare |
| East Asian | 0.00092 | 0.00092 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.00017 | 0.00017 | rare |
| South Asian | 0.00013 | 0.00013 | rare |
| Other | 0.00033 | 0.00033 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: SNARE involved in vesicular transport from the late endosomes to the trans-Golgi network. {ECO:0000269|PubMed:18195106}.;
Recessive Scores
- pRec
- 0.121
Intolerance Scores
- LoFtool
- 0.327
- RVIS EVS
- -0.07
- RVIS percentile EVS
- 48.35
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.852
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |