SYTL5
protein-codingsynaptotagmin like 5, the group of Synaptotagmin like tandem C2 proteins
Gene summary
The protein encoded by this gene belongs to the synaptotagmin-like (Slp) protein family, which contains a unique homology domain at the N-terminus, referred to as the Slp homology domain (SHD). The SHD functions as a binding site for Rab27A, which plays a role in protein transport. Expression of this gene is restricted to placenta and liver, suggesting that it might be involved in Rab27A-dependent membrane trafficking in specific tissues. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2009]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~122.3 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to SYTL5 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_138780.3. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 11 | 1 | 12 | |||
| missense | 115 | 9 | 1 | 125 | ||
| nonsense | 7 | 7 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 13 | 13 | ||||
| Total | 0 | 0 | 146 | 10 | 1 | 157 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_620135.1 | 16 | MANE Select | |
| Ensembl | ENSP00000297875.2 | 16 | MANE Select | |
| RefSeq | NP_001156806.1 | 17 | Standard | |
| RefSeq | NP_001156807.1 | 16 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Deregulation of Rab and Rab Effector Genes in Bladder Cancer
Biological Process
- intracellular protein transport
- exocytosis
Molecular Function
- protein binding
- phospholipid binding
- Rab GTPase binding
- metal ion binding
Cellular Component
- membrane
- exocytic vesicle
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000456733
- Coding exons
- 17
- Length
- 122238
- Individuals with no LoFs
- 125722
- Homozygous LoFs
- 6
- Heterozygous LoFs
- 10
- Defined
- 125738
- p
- 0.0000636
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.389 | 286 | 268 | 1.07 | 0.0000204 | 4915 |
| Missense (PolyPhen) | 97 | 89.409 | 1.0849 | 1670 | ||
| Synonymous | -1.24 | 107 | 91.8 | 1.17 | 0.00000655 | 1418 |
| Loss of Function | 2.99 | 11 | 28.1 | 0.392 | 0.00000224 | 509 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000076 | 0.000062 | rare |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00022 | 0.00016 | rare |
| Finnish | 0.000065 | 0.000046 | rare |
| European (Non-Finnish) | 0.00010 | 0.000070 | rare |
| South Asian | 0.00016 | 0.000098 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: May act as Rab effector protein and play a role in vesicle trafficking. Binds phospholipids.;
Recessive Scores
- pRec
- 0.107
Intolerance Scores
- LoFtool
- 0.741
- RVIS EVS
- 0.56
- RVIS percentile EVS
- 81.63
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.697
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |