SYT4
synaptotagmin 4, the group of Synaptotagmins
Basic information
Region (hg38): 18:43267892-43277535
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (35 variants)
- not_provided (3 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the SYT4 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000020783.4. 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 | 33 | 36 | ||||
| nonsense | 0 | |||||
| start loss | 1 | 1 | ||||
| frameshift | 1 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 35 | 3 | 0 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| SYT4 | protein_coding | protein_coding | ENST00000255224 | 4 | 9773 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.439 | 0.560 | 125688 | 0 | 18 | 125706 | 0.0000716 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.0635 | 213 | 216 | 0.988 | 0.0000102 | 2779 |
| Missense in Polyphen | 74 | 86.452 | 0.85596 | 1161 | ||
| Synonymous | -1.17 | 100 | 86.2 | 1.16 | 0.00000431 | 831 |
| Loss of Function | 2.74 | 3 | 14.1 | 0.212 | 7.19e-7 | 211 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000124 | 0.000124 |
| Ashkenazi Jewish | 0.000695 | 0.000695 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000617 | 0.0000616 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.000163 | 0.000163 |
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 (By similarity). Plays a role in dendrite formation by melanocytes (PubMed:23999003). {ECO:0000250|UniProtKB:P50232, ECO:0000269|PubMed:23999003}.;
Recessive Scores
- pRec
- 0.148
Intolerance Scores
- loftool
- 0.609
- rvis_EVS
- 0.02
- rvis_percentile_EVS
- 55.22
Haploinsufficiency Scores
- pHI
- 0.305
- hipred
- Y
- hipred_score
- 0.712
- ghis
- 0.575
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.945
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Syt4
- Phenotype
- behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan);
Gene ontology
- Biological process
- brain development;memory;positive regulation of glutamate secretion;regulation of dopamine secretion;vesicle-mediated transport;calcium ion regulated exocytosis;regulation of calcium ion-dependent exocytosis;regulation of endocytosis;negative regulation of vesicle fusion;negative regulation of catecholamine secretion;negative regulation of calcium ion-dependent exocytosis;positive regulation of calcium ion-dependent exocytosis;negative regulation of short-term neuronal synaptic plasticity;calcium ion-regulated exocytosis of neurotransmitter;negative regulation of protein secretion;vesicle fusion with vesicle;secretory granule maturation;cellular response to calcium ion;regulation of presynaptic dense core granule exocytosis;trans-synaptic signaling by BDNF, modulating synaptic transmission;positive regulation of dendrite extension;negative regulation of dense core granule exocytosis;positive regulation of dense core granule exocytosis;negative regulation of retrograde trans-synaptic signaling by neuropeptide;negative regulation of synaptic vesicle exocytosis
- Cellular component
- plasma membrane;cell junction;integral component of Golgi membrane;integral component of synaptic vesicle membrane;axon;dendrite;dense core granule membrane;neuron projection;neuronal cell body;intracellular membrane-bounded organelle;neuron projection terminus;perinuclear region of cytoplasm;exocytic vesicle;astrocyte projection;glutamatergic synapse;integral component of neuronal dense core vesicle membrane;microvesicle
- Molecular function
- SNARE binding;phosphatidylserine binding;calcium ion binding;protein binding;calcium-dependent phospholipid binding;syntaxin-1 binding;clathrin binding;syntaxin-3 binding;protein homodimerization activity;protein heterodimerization activity