STX17
syntaxin 17, the group of Syntaxins
Basic information
Region (hg38): 9:99906654-99974534
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the STX17 gene is commonly pathogenic or not.
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.
| Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 21 | 21 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 21 | 0 | 0 |
Variants in STX17
This is a list of pathogenic ClinVar variants found in the STX17 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 9-99915246-G-A | not specified | Uncertain significance (Jan 04, 2022) | ||
| 9-99915270-C-T | not specified | Uncertain significance (Jul 12, 2022) | ||
| 9-99915274-G-A | not specified | Uncertain significance (Apr 13, 2022) | ||
| 9-99915316-C-T | not specified | Uncertain significance (May 06, 2024) | ||
| 9-99915343-A-G | not specified | Uncertain significance (May 31, 2023) | ||
| 9-99915361-A-G | not specified | Uncertain significance (Dec 13, 2022) | ||
| 9-99928809-A-G | not specified | Uncertain significance (Feb 12, 2024) | ||
| 9-99928832-C-T | not specified | Uncertain significance (Jun 21, 2022) | ||
| 9-99951109-G-A | not specified | Uncertain significance (Jul 13, 2021) | ||
| 9-99951130-T-G | not specified | Uncertain significance (Aug 27, 2024) | ||
| 9-99951207-G-A | not specified | Uncertain significance (Aug 04, 2024) | ||
| 9-99951253-A-G | not specified | Uncertain significance (May 23, 2024) | ||
| 9-99959954-G-T | not specified | Uncertain significance (Nov 21, 2022) | ||
| 9-99960144-C-T | not specified | Uncertain significance (Jul 26, 2022) | ||
| 9-99967726-A-G | not specified | Uncertain significance (May 22, 2023) | ||
| 9-99968482-G-T | not specified | Uncertain significance (May 03, 2023) | ||
| 9-99968503-A-G | not specified | Uncertain significance (Mar 19, 2024) | ||
| 9-99968503-A-T | not specified | Uncertain significance (Sep 07, 2022) | ||
| 9-99968509-C-A | not specified | Uncertain significance (Mar 07, 2024) | ||
| 9-99968557-G-A | not specified | Uncertain significance (Jun 16, 2024) | ||
| 9-99968614-G-A | not specified | Uncertain significance (Dec 06, 2022) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| STX17 | protein_coding | protein_coding | ENST00000259400 | 7 | 63704 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0000946 | 0.943 | 125714 | 0 | 33 | 125747 | 0.000131 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.594 | 136 | 157 | 0.867 | 0.00000765 | 1976 |
| Missense in 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 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000529 | 0.000529 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.0000462 | 0.0000462 |
| European (Non-Finnish) | 0.000115 | 0.000114 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000664 | 0.0000653 |
| Other | 0.000163 | 0.000163 |
dbNSFP
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}.;
- Pathway
- Autophagy - animal - Homo sapiens (human);SNARE interactions in vesicular transport - Homo sapiens (human);Nicotine Pathway (Dopaminergic Neuron), Pharmacodynamics;Vesicle-mediated transport;Membrane Trafficking;Post-translational protein modification;Metabolism of proteins;Transport to the Golgi and subsequent modification;Asparagine N-linked glycosylation;COPII-mediated vesicle transport;ER to Golgi Anterograde Transport
(Consensus)
Recessive Scores
- pRec
- 0.119
Intolerance Scores
- loftool
- 0.473
- rvis_EVS
- 0.15
- rvis_percentile_EVS
- 64.32
Haploinsufficiency Scores
- pHI
- 0.196
- hipred
- Y
- hipred_score
- 0.543
- ghis
- 0.568
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.801
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Stx17
- Phenotype
Gene ontology
- Biological process
- intracellular protein transport;endoplasmic reticulum to Golgi vesicle-mediated transport;vesicle fusion;Golgi organization;autophagosome membrane docking;protein localization to phagophore assembly site;vesicle docking;endoplasmic reticulum-Golgi intermediate compartment organization;autophagosome maturation
- Cellular component
- autophagosome membrane;mitochondrion;lysosomal membrane;autophagosome;endoplasmic reticulum membrane;rough endoplasmic reticulum;endoplasmic reticulum-Golgi intermediate compartment;cytosol;endomembrane system;ER to Golgi transport vesicle membrane;integral component of membrane;COPII-coated ER to Golgi transport vesicle;smooth endoplasmic reticulum membrane;HOPS complex;SNARE complex;endoplasmic reticulum-Golgi intermediate compartment membrane;mitochondria-associated endoplasmic reticulum membrane
- Molecular function
- SNARE binding;SNAP receptor activity;protein binding;protein kinase binding;protein phosphatase binding