CPLX3
protein-codingcomplexin 3
Gene summary
Predicted to enable SNARE binding activity. Predicted to be involved in modulation of chemical synaptic transmission; regulation of synaptic vesicle fusion to presynaptic active zone membrane; and synaptic vesicle tethering involved in synaptic vesicle exocytosis. Predicted to act upstream of or within regulation of neurotransmitter secretion. Predicted to be located in cytosol; plasma membrane; and synapse. Predicted to be part of SNARE complex. Predicted to be active in terminal bouton. [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 ~5.2 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 CPLX3 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001030005.3. 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 | 0 | |||||
| missense | 25 | 25 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 25 | 0 | 0 | 25 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001025176.1 | 3 | MANE Select | |
| Ensembl | ENSP00000378464.4 | 3 | MANE Select | |
| Ensembl | ENSP00000773822.1 | 3 | Standard | |
| Ensembl | ENSP00000811784.1 | 3 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Synaptic vesicle cycle - Homo sapiens (human)
- Synaptic Vesicle Pathway
Biological Process
- synaptic vesicle exocytosis
- insulin secretion
- regulation of synaptic vesicle fusion to presynaptic active zone membrane
- regulation of neurotransmitter secretion
Molecular Function
- SNARE binding
- neurotransmitter transporter activity
- syntaxin binding
Cellular Component
- cytosol
- cell junction
- SNARE complex
- terminal bouton
- photoreceptor ribbon synapse
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000395018
- Coding exons
- 3
- Length
- 5254
- Individuals with no LoFs
- 125683
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 13
- Defined
- 125696
- p
- 0.0000517
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.513 | 81 | 95.1 | 0.852 | 0.00000541 | 1025 |
| Missense (PolyPhen) | 28 | 36.288 | 0.77161 | 410 | ||
| Synonymous | 0.310 | 35 | 37.4 | 0.935 | 0.00000209 | 295 |
| Loss of Function | 1.84 | 2 | 7.39 | 0.271 | 3.98e-7 | 83 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.0000094 | 0.0000088 | rare |
| South Asian | 0.00039 | 0.00036 | rare |
| Other | 0.00018 | 0.00016 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Positively regulates a late step in synaptic vesicle exocytosis. {ECO:0000250}.;
Intolerance Scores
- LoFtool
- 0.246
- RVIS EVS
- 0.01
- RVIS percentile EVS
- 54.95
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.614
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |