SYT5
synaptotagmin 5, the group of Synaptotagmins
Basic information
Region (hg38): 19:55171196-55180289
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 SYT5 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 | 29 | 29 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 29 | 0 | 0 |
Variants in SYT5
This is a list of pathogenic ClinVar variants found in the SYT5 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 19-55173557-T-C | not specified | Uncertain significance (Sep 14, 2022) | ||
| 19-55173570-C-A | not specified | Uncertain significance (Jan 29, 2024) | ||
| 19-55173591-C-A | not specified | Uncertain significance (Dec 14, 2024) | ||
| 19-55173648-T-C | not specified | Uncertain significance (Feb 28, 2023) | ||
| 19-55173672-C-T | not specified | Uncertain significance (Dec 22, 2023) | ||
| 19-55174522-C-T | not specified | Uncertain significance (Dec 14, 2023) | ||
| 19-55174561-A-G | not specified | Uncertain significance (Aug 17, 2022) | ||
| 19-55174563-T-C | not specified | Uncertain significance (Nov 22, 2021) | ||
| 19-55174609-C-T | not specified | Uncertain significance (Feb 01, 2025) | ||
| 19-55174612-T-C | not specified | Uncertain significance (Jun 28, 2024) | ||
| 19-55174642-C-T | not specified | Uncertain significance (May 13, 2024) | ||
| 19-55174884-G-A | not specified | Uncertain significance (Jul 23, 2024) | ||
| 19-55174947-C-G | not specified | Uncertain significance (Sep 20, 2023) | ||
| 19-55175179-C-T | not specified | Uncertain significance (Sep 21, 2023) | ||
| 19-55175185-G-A | not specified | Uncertain significance (Oct 08, 2024) | ||
| 19-55175230-A-G | not specified | Uncertain significance (Jun 10, 2024) | ||
| 19-55175268-A-T | not specified | Uncertain significance (Aug 15, 2024) | ||
| 19-55175285-C-A | not specified | Uncertain significance (Sep 04, 2024) | ||
| 19-55175336-G-A | not specified | Uncertain significance (Feb 07, 2025) | ||
| 19-55175720-A-C | not specified | Uncertain significance (Feb 21, 2025) | ||
| 19-55175759-C-G | not specified | Uncertain significance (Mar 31, 2024) | ||
| 19-55175780-G-C | not specified | Uncertain significance (Feb 28, 2024) | ||
| 19-55175842-G-C | not specified | Uncertain significance (May 24, 2024) | ||
| 19-55175852-T-C | not specified | Uncertain significance (Oct 20, 2021) | ||
| 19-55176071-C-G | not specified | Uncertain significance (Jul 20, 2021) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| SYT5 | protein_coding | protein_coding | ENST00000354308 | 8 | 9243 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.00190 | 0.978 | 125712 | 0 | 36 | 125748 | 0.000143 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.19 | 168 | 218 | 0.772 | 0.0000134 | 2431 |
| Missense in Polyphen | 52 | 79.666 | 0.65273 | 905 | ||
| Synonymous | 0.731 | 87 | 96.1 | 0.905 | 0.00000604 | 813 |
| Loss of Function | 2.04 | 7 | 15.7 | 0.445 | 7.40e-7 | 192 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000918 | 0.0000918 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.0000927 | 0.0000924 |
| European (Non-Finnish) | 0.000262 | 0.000246 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000477 | 0.0000327 |
| Other | 0.000331 | 0.000326 |
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. Regulates the Ca(2+)- dependent secretion of norepinephrine in PC12 cells. Required for export from the endocytic recycling compartment to the cell surface (By similarity). {ECO:0000250}.;
Recessive Scores
- pRec
- 0.175
Intolerance Scores
- loftool
- 0.790
- rvis_EVS
- 0.02
- rvis_percentile_EVS
- 55.45
Haploinsufficiency Scores
- pHI
- 0.168
- hipred
- N
- hipred_score
- 0.487
- ghis
- 0.533
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.325
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Syt5
- Phenotype
- nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); normal phenotype;
Gene ontology
- Biological process
- chemical synaptic transmission;regulation of dopamine secretion;synaptic vesicle exocytosis;vesicle-mediated transport;calcium ion regulated exocytosis;regulation of calcium ion-dependent exocytosis;synaptic vesicle endocytosis;calcium ion-regulated exocytosis of neurotransmitter;cellular response to calcium ion
- Cellular component
- plasma membrane;cell junction;axon;synaptic vesicle membrane;dense core granule;neuronal cell body;perinuclear region of cytoplasm;recycling endosome membrane;exocytic vesicle;integral component of neuronal dense core vesicle membrane;proximal neuron projection
- Molecular function
- SNARE binding;phosphatidylserine binding;calcium ion binding;calcium-dependent phospholipid binding;phosphatidylinositol-4,5-bisphosphate binding;syntaxin binding;clathrin binding;protein heterodimerization activity