STX18
Basic information
Region (hg38): 4:4415742-4542346
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (52 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the STX18 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000016930.4. Only rare variants are included in the table.
In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.
Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 51 | 52 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 51 | 1 | 0 |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| STX18 | protein_coding | protein_coding | ENST00000306200 | 11 | 126605 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 2.49e-7 | 0.911 | 125706 | 0 | 42 | 125748 | 0.000167 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.698 | 158 | 185 | 0.855 | 0.00000956 | 2203 |
| Missense in Polyphen | 30 | 33.464 | 0.89649 | 430 | ||
| Synonymous | -0.771 | 78 | 69.8 | 1.12 | 0.00000402 | 606 |
| Loss of Function | 1.72 | 14 | 22.9 | 0.612 | 0.00000134 | 247 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000366 | 0.000362 |
| Ashkenazi Jewish | 0.000198 | 0.000198 |
| East Asian | 0.000326 | 0.000326 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.000163 | 0.000158 |
| Middle Eastern | 0.000326 | 0.000326 |
| South Asian | 0.000271 | 0.000261 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Syntaxin that may be involved in targeting and fusion of Golgi-derived retrograde transport vesicles with the ER. {ECO:0000269|PubMed:15029241}.;
- Pathway
- Phagosome - Homo sapiens (human);SNARE interactions in vesicular transport - Homo sapiens (human);Nicotine Pathway (Dopaminergic Neuron), Pharmacodynamics;Vesicle-mediated transport;Membrane Trafficking;COPI-dependent Golgi-to-ER retrograde traffic;Golgi-to-ER retrograde transport;Intra-Golgi and retrograde Golgi-to-ER traffic
(Consensus)
Recessive Scores
- pRec
- 0.161
Intolerance Scores
- loftool
- 0.786
- rvis_EVS
- 0.08
- rvis_percentile_EVS
- 60.31
Haploinsufficiency Scores
- pHI
- 0.153
- hipred
- Y
- hipred_score
- 0.602
- ghis
- 0.556
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.878
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Stx18
- Phenotype
- embryo phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); homeostasis/metabolism phenotype; growth/size/body region phenotype;
Gene ontology
- Biological process
- intracellular protein transport;retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum;membrane fusion;endoplasmic reticulum membrane organization;positive regulation of organelle assembly;positive regulation of ER to Golgi vesicle-mediated transport;regulation of Golgi organization
- Cellular component
- Golgi membrane;endoplasmic reticulum;endoplasmic reticulum membrane;integral component of membrane;SNARE complex
- Molecular function
- SNAP receptor activity;protein binding;protein domain specific binding