SYT9
Basic information
Region (hg38): 11:7238778-7469043
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (48 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the SYT9 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000175733.4. 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 | 46 | 48 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 46 | 2 | 0 |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| SYT9 | protein_coding | protein_coding | ENST00000318881 | 7 | 230265 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.309 | 0.691 | 125733 | 0 | 15 | 125748 | 0.0000596 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.32 | 211 | 272 | 0.776 | 0.0000155 | 3216 |
| Missense in Polyphen | 77 | 118.84 | 0.64792 | 1414 | ||
| Synonymous | -0.117 | 115 | 113 | 1.01 | 0.00000696 | 956 |
| Loss of Function | 3.29 | 5 | 21.4 | 0.233 | 0.00000128 | 245 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000148 | 0.000148 |
| Ashkenazi Jewish | 0.0000992 | 0.0000992 |
| East Asian | 0.0000544 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000529 | 0.0000527 |
| Middle Eastern | 0.0000544 | 0.0000544 |
| South Asian | 0.0000980 | 0.0000980 |
| 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.;
- Pathway
- Vesicle-mediated transport;Membrane Trafficking;Neuronal System;Clathrin-mediated endocytosis;Neurexins and neuroligins;Cargo recognition for clathrin-mediated endocytosis;Protein-protein interactions at synapses
(Consensus)
Recessive Scores
- pRec
- 0.120
Intolerance Scores
- loftool
- 0.546
- rvis_EVS
- -0.07
- rvis_percentile_EVS
- 48.54
Haploinsufficiency Scores
- pHI
- 0.359
- hipred
- Y
- hipred_score
- 0.749
- ghis
- 0.616
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.742
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Syt9
- Phenotype
Gene ontology
- Biological process
- regulation of dopamine secretion;vesicle-mediated transport;calcium ion regulated exocytosis;regulation of calcium ion-dependent exocytosis;regulation of insulin secretion;membrane organization;cellular response to calcium ion;calcium-dependent activation of synaptic vesicle fusion
- Cellular component
- plasma membrane;cell junction;integral component of synaptic vesicle membrane;clathrin-coated vesicle membrane;secretory granule membrane;dense core granule;exocytic vesicle;hippocampal mossy fiber to CA3 synapse
- Molecular function
- SNARE binding;phosphatidylserine binding;calcium ion binding;calcium-dependent phospholipid binding;phosphatidylinositol-4,5-bisphosphate binding;syntaxin binding;clathrin binding;identical protein binding