SYBU
protein-codingsyntabulin
Gene summary
Syntabulin/GOLSYN is part of a kinesin motor-adaptor complex that is critical for the anterograde axonal transport of active zone components and contributes to activity-dependent presynaptic assembly during neuronal development (Cai et al., 2007 [PubMed 17611281]).[supplied by OMIM, Mar 2008]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~117.8 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 SYBU variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001099754.2. 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 | 1 | 2 | 3 | |||
| missense | 100 | 4 | 1 | 105 | ||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 2 | 2 | ||||
| Total | 0 | 0 | 103 | 4 | 3 | 110 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001093224.1 | 7 | MANE Select | |
| Ensembl | ENSP00000276646.9 | 7 | MANE Select | |
| RefSeq | NP_001093213.1 | 7 | Standard | |
| RefSeq | NP_001093214.1 | 7 | Standard |
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| sybu | Danio rerio | Structure: whole organism Quality: wholly ventralized abnormal |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- axonal transport of mitochondrion
- positive regulation of insulin secretion involved in cellular response to glucose stimulus
- regulation of synaptic activity
- synapse maturation
- anterograde neuronal dense core vesicle transport
Molecular Function
- protein binding
- microtubule binding
- syntaxin-1 binding
- kinesin binding
Cellular Component
- Golgi membrane
- microtubule
- integral component of membrane
- cytoplasmic vesicle
- vesicle
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000422135
- Coding exons
- 7
- Length
- 117814
- Individuals with no LoFs
- 124775
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 30
- Defined
- 124805
- p
- 0.000120
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.08 | 330 | 390 | 0.847 | 0.0000229 | 4321 |
| Missense (PolyPhen) | 119 | 160.09 | 0.74334 | 1807 | ||
| Synonymous | -0.462 | 163 | 156 | 1.05 | 0.00000958 | 1344 |
| Loss of Function | 2.64 | 11 | 25.4 | 0.434 | 0.00000154 | 292 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000065 | 0.000065 | rare |
| Latino/Admixed American | 0.00029 | 0.00029 | rare |
| Ashkenazi Jewish | 0.000099 | 0.000099 | rare |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0.00014 | 0.00014 | rare |
| European (Non-Finnish) | 0.00013 | 0.00012 | rare |
| South Asian | 0.000033 | 0.000033 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Part of a kinesin motor-adapter complex that is critical for the anterograde axonal transport of active zone components and contributes to activity-dependent presynaptic assembly during neuronal development. {ECO:0000250, ECO:0000269|PubMed:15459722}.;
Intolerance Scores
- RVIS EVS
- -0.2
- RVIS percentile EVS
- 39.11
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.539
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |