SV2C
protein-codingsynaptic vesicle glycoprotein 2C, the group of Solute carrier family 22
Gene summary
Predicted to enable transmembrane transporter activity. Predicted to be involved in regulation of synaptic vesicle exocytosis. Located in nucleoplasm. [provided by Alliance of Genome Resources, Jun 2026]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~270.6 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 SV2C variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_014979.4. 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 | 7 | 2 | 9 | |||
| missense | 101 | 6 | 1 | 108 | ||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 101 | 13 | 3 | 117 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_055794.3 | 12 | MANE Select | |
| Ensembl | ENSP00000423541.2 | 12 | MANE Select | |
| RefSeq | NP_001284645.1 | 12 | Standard | |
| Ensembl | ENSP00000316983.7 | 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
- plasma membrane
- synaptic vesicle
- integral component of membrane
- cell junction
- integral component of synaptic vesicle membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000502798
- Coding exons
- 12
- Length
- 270768
- Individuals with no LoFs
- 125274
- Homozygous LoFs
- 1
- Heterozygous LoFs
- 77
- Defined
- 125352
- p
- 0.000311
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.868 | 369 | 419 | 0.881 | 0.0000232 | 4794 |
| Missense (PolyPhen) | 143 | 174.38 | 0.82007 | 1952 | ||
| Synonymous | -1.40 | 184 | 161 | 1.14 | 0.00000969 | 1363 |
| Loss of Function | 3.28 | 14 | 34.9 | 0.401 | 0.00000166 | 415 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000065 | 0.000063 | rare |
| Latino/Admixed American | 0.0012 | 0.0011 | notable |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00028 | 0.00027 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.00019 | 0.00018 | rare |
| South Asian | 0.00039 | 0.00039 | rare |
| Other | 0.00017 | 0.00016 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Plays a role in the control of regulated secretion in neural and endocrine cells, enhancing selectively low-frequency neurotransmission. Positively regulates vesicle fusion by maintaining the readily releasable pool of secretory vesicles. {ECO:0000250|UniProtKB:Q9Z2I6}.; FUNCTION: (Microbial infection) Possible receptor for C.botulinum neurotoxin type D (BoNT/D, botD); note that type D does not usually infect humans. {ECO:0000269|PubMed:21483489}.;
Recessive Scores
- pRec
- 0.136
Intolerance Scores
- RVIS EVS
- -0.24
- RVIS percentile EVS
- 36.28
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- S
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.685
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |