SV2B
protein-codingsynaptic vesicle glycoprotein 2B, the group of Solute carrier family 22
Gene summary
This gene encodes a member of the synaptic vesicle proteins 2 (SV2) family and major facilitator superfamily of proteins. This protein and other members of the family are localized to synaptic vesicles and may function in the regulation of vesicle trafficking and exocytosis. Studies in mice suggest that the encoded protein may act as a protein receptor for botulinum neurotoxin E in neurons, and that this protein may be important for the integrity of the glomerular filtration barrier. This gene shows reduced expression in areas of synaptic loss in the hippocampus of human temporal lobe epilepsy patients. [provided by RefSeq, Sep 2016]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~202.6 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 SV2B variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001323032.3. 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 | 1 | 1 | ||||
| missense | 97 | 2 | 99 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 97 | 3 | 0 | 100 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001309961.1 | 12 | MANE Select | |
| Ensembl | ENSP00000377779.1 | 12 | MANE Select | |
| RefSeq | NP_001161052.1 | 11 | Standard | |
| RefSeq | NP_001309960.1 | 12 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- ECM-receptor interaction - Homo sapiens (human)
- Disease
- Toxicity of botulinum toxin type A (BoNT/A)
- Toxicity of botulinum toxin type D (BoNT/D)
- Toxicity of botulinum toxin type F (BoNT/F)
Biological Process
- neurotransmitter transport
- chemical synaptic transmission
- transmembrane transport
Molecular Function
- protein binding
- transmembrane transporter activity
Cellular Component
- acrosomal vesicle
- plasma membrane
- synaptic vesicle
- membrane
- integral component of membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000394232
- Coding exons
- 12
- Length
- 201360
- Individuals with no LoFs
- 125719
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 29
- Defined
- 125748
- p
- 0.000115
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.16 | 327 | 392 | 0.835 | 0.0000209 | 4560 |
| Missense (PolyPhen) | 104 | 146.42 | 0.71028 | 1745 | ||
| Synonymous | 0.825 | 139 | 152 | 0.915 | 0.00000885 | 1269 |
| Loss of Function | 3.20 | 13 | 32.7 | 0.397 | 0.00000165 | 368 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000062 | 0.000062 | rare |
| Latino/Admixed American | 0.00014 | 0.00014 | rare |
| Ashkenazi Jewish | 0.00040 | 0.00040 | rare |
| East Asian | 0.00016 | 0.00016 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000079 | 0.000079 | rare |
| South Asian | 0.00013 | 0.00013 | rare |
| Other | 0.00050 | 0.00049 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Probably plays a role in the control of regulated secretion in neural and endocrine cells. {ECO:0000250}.;
Recessive Scores
- pRec
- 0.177
Intolerance Scores
- LoFtool
- 0.468
- RVIS EVS
- -1.17
- RVIS percentile EVS
- 5.99
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.734
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |