STX7
syntaxin 7, the group of Syntaxins
Basic information
Region (hg38): 6:132445867-132513198
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 STX7 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 | 8 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 8 | 0 | 0 |
Variants in STX7
This is a list of pathogenic ClinVar variants found in the STX7 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 6-132460772-C-T | not specified | Uncertain significance (Nov 13, 2023) | ||
| 6-132460820-T-G | not specified | Uncertain significance (Sep 02, 2024) | ||
| 6-132464010-T-C | not specified | Uncertain significance (Mar 07, 2024) | ||
| 6-132464058-C-T | not specified | Uncertain significance (Dec 07, 2024) | ||
| 6-132469991-C-T | not specified | Uncertain significance (Oct 29, 2021) | ||
| 6-132470018-T-C | not specified | Uncertain significance (May 01, 2024) | ||
| 6-132471510-G-C | not specified | Uncertain significance (Nov 22, 2024) | ||
| 6-132471543-T-C | not specified | Uncertain significance (Jun 07, 2023) | ||
| 6-132471586-T-C | not specified | Uncertain significance (Nov 14, 2024) | ||
| 6-132471597-G-C | not specified | Uncertain significance (Feb 09, 2022) | ||
| 6-132472292-G-C | not specified | Uncertain significance (Mar 19, 2024) | ||
| 6-132472323-T-C | not specified | Uncertain significance (May 28, 2024) | ||
| 6-132472361-T-C | not specified | Uncertain significance (Dec 06, 2022) | ||
| 6-132472372-T-G | Abnormality of neuronal migration | Likely pathogenic (Oct 31, 2014) | ||
| 6-132503451-T-A | not specified | Uncertain significance (Oct 11, 2023) | ||
| 6-132503517-G-A | not specified | Uncertain significance (Aug 04, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| STX7 | protein_coding | protein_coding | ENST00000367941 | 9 | 67332 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.00000503 | 0.871 | 125727 | 0 | 17 | 125744 | 0.0000676 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.811 | 110 | 137 | 0.805 | 0.00000686 | 1718 |
| Missense in Polyphen | 37 | 48.79 | 0.75835 | 654 | ||
| Synonymous | -0.239 | 46 | 44.0 | 1.05 | 0.00000214 | 463 |
| Loss of Function | 1.49 | 11 | 17.8 | 0.618 | 9.07e-7 | 199 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000590 | 0.0000590 |
| Ashkenazi Jewish | 0.0000998 | 0.0000992 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.000116 | 0.000114 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000336 | 0.0000327 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: May be involved in protein trafficking from the plasma membrane to the early endosome (EE) as well as in homotypic fusion of endocytic organelles. Mediates the endocytic trafficking from early endosomes to late endosomes and lysosomes.;
- Pathway
- Phagosome - Homo sapiens (human);SNARE interactions in vesicular transport - Homo sapiens (human);Nicotine Pathway (Dopaminergic Neuron), Pharmacodynamics;miR-targeted genes in epithelium - TarBase;miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase
(Consensus)
Recessive Scores
- pRec
- 0.166
Intolerance Scores
- loftool
- 0.682
- rvis_EVS
- -0.1
- rvis_percentile_EVS
- 46.49
Haploinsufficiency Scores
- pHI
- 0.162
- hipred
- Y
- hipred_score
- 0.765
- ghis
- 0.558
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.680
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Stx7
- Phenotype
Gene ontology
- Biological process
- positive regulation of T cell mediated cytotoxicity;intracellular protein transport;vesicle fusion;vesicle docking;organelle localization;organelle assembly;positive regulation of receptor localization to synapse;regulation of protein localization to plasma membrane
- Cellular component
- immunological synapse;lysosome;lysosomal membrane;endosome;early endosome;late endosome;plasma membrane;synaptic vesicle;endomembrane system;integral component of membrane;endocytic vesicle;SNARE complex;early endosome membrane;vesicle;azurophil granule;perinuclear region of cytoplasm;recycling endosome;extracellular exosome;tertiary granule
- Molecular function
- SNARE binding;SNAP receptor activity;protein binding;chloride channel inhibitor activity;syntaxin binding