SYT11
Basic information
Region (hg38): 1:155859567-155885199
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (37 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the SYT11 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000152280.5. 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 | 37 | 38 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 37 | 1 | 0 |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| SYT11 | protein_coding | protein_coding | ENST00000368324 | 4 | 25691 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.927 | 0.0732 | 125735 | 0 | 2 | 125737 | 0.00000795 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.68 | 178 | 253 | 0.703 | 0.0000142 | 2826 |
| Missense in Polyphen | 68 | 114.03 | 0.59632 | 1280 | ||
| Synonymous | 0.962 | 90 | 102 | 0.879 | 0.00000600 | 882 |
| Loss of Function | 3.05 | 1 | 12.7 | 0.0784 | 6.29e-7 | 163 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000615 | 0.0000615 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.0000462 | 0.0000462 |
| European (Non-Finnish) | 0.00 | 0.00 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: May be involved in Ca(2+)-dependent exocytosis of secretory vesicles through Ca(2+) and phospholipid binding to the C2 domain or may serve as Ca(2+) sensors in the process of vesicular trafficking and exocytosis. {ECO:0000250}.;
- Pathway
- Parkinsons Disease Pathway;Vesicle-mediated transport;Membrane Trafficking;Clathrin-mediated endocytosis;Cargo recognition for clathrin-mediated endocytosis
(Consensus)
Recessive Scores
- pRec
- 0.149
Intolerance Scores
- loftool
- 0.0933
- rvis_EVS
- -0.25
- rvis_percentile_EVS
- 35.99
Haploinsufficiency Scores
- pHI
- 0.519
- hipred
- Y
- hipred_score
- 0.673
- ghis
- 0.582
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.861
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Syt11
- Phenotype
- normal phenotype;
Gene ontology
- Biological process
- plasma membrane repair;regulation of dopamine secretion;vesicle-mediated transport;calcium ion regulated exocytosis;regulation of calcium ion-dependent exocytosis;negative regulation of neurotransmitter secretion;calcium ion-regulated exocytosis of neurotransmitter;negative regulation of phagocytosis;protein homotetramerization;cellular response to calcium ion;negative regulation of interleukin-6 secretion;negative regulation of clathrin-dependent endocytosis;negative regulation of synaptic vesicle endocytosis;regulation of defense response to bacterium;negative regulation of tumor necrosis factor secretion;negative regulation of membrane invagination;regulation of phagosome maturation;positive regulation of protein localization to phagocytic vesicle;negative regulation of clathrin-coated pit assembly;calcium ion regulated lysosome exocytosis
- Cellular component
- phagocytic cup;lysosome;plasma membrane;synaptic vesicle;postsynaptic density;cell junction;integral component of synaptic vesicle membrane;axon;early phagosome;neuron projection;terminal bouton;dendritic spine;cell body;phagocytic vesicle;perinuclear region of cytoplasm;presynaptic active zone membrane;recycling endosome;excitatory synapse;inhibitory synapse;exocytic vesicle;Schaffer collateral - CA1 synapse;presynapse;integral component of presynaptic active zone membrane
- Molecular function
- SNARE binding;phosphatidylserine binding;calcium ion binding;protein binding;calcium-dependent phospholipid binding;clathrin binding;translation initiation factor binding;ubiquitin protein ligase binding;protein homodimerization activity;beta-tubulin binding