CPLX1
complexin 1
Basic information
Region (hg38): 4:784957-826129
Links
Phenotypes
GenCC
Source:
- familial infantile myoclonic epilepsy (Supportive), mode of inheritance: AR
- developmental and epileptic encephalopathy, 63 (Strong), mode of inheritance: AR
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Developmental and epileptic encephalopathy 63 | AR | General | Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing | Neurologic | 26539891; 28422131 |
ClinVar
This is a list of variants' phenotypes submitted to
- not_provided (53 variants)
- Inborn_genetic_diseases (21 variants)
- Developmental_and_epileptic_encephalopathy,_63 (6 variants)
- CPLX1-related_disorder (5 variants)
- 4p_partial_monosomy_syndrome (1 variants)
- Abnormal_brain_morphology (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the CPLX1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000006651.4. Only rare variants are included in the table.
In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.
Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 19 | 19 | ||||
| missense | 34 | 36 | ||||
| nonsense | 3 | |||||
| start loss | 0 | |||||
| frameshift | 1 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 4 | 35 | 20 | 0 |
Highest pathogenic variant AF is 0.00007251441
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| CPLX1 | protein_coding | protein_coding | ENST00000304062 | 3 | 41242 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.825 | 0.172 | 122001 | 0 | 3 | 122004 | 0.0000123 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | -0.351 | 93 | 83.9 | 1.11 | 0.00000463 | 871 |
| Missense in Polyphen | 48 | 38.58 | 1.2442 | 401 | ||
| Synonymous | -1.98 | 51 | 35.9 | 1.42 | 0.00000219 | 238 |
| Loss of Function | 2.22 | 0 | 5.75 | 0.00 | 2.44e-7 | 75 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000273 | 0.0000273 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Positively regulates a late step in exocytosis of various cytoplasmic vesicles, such as synaptic vesicles and other secretory vesicles (PubMed:21785414). Organizes the SNAREs into a cross-linked zigzag topology that, when interposed between the vesicle and plasma membranes, is incompatible with fusion, thereby preventing SNAREs from releasing neurotransmitters until an action potential arrives at the synapse (PubMed:21785414). Also involved in glucose-induced secretion of insulin by pancreatic beta-cells. Essential for motor behavior. {ECO:0000250|UniProtKB:P63040, ECO:0000269|PubMed:21785414}.;
- Pathway
- Synaptic vesicle cycle - Homo sapiens (human);Synaptic Vesicle Pathway;Neuronal System;Glutamate Neurotransmitter Release Cycle;Dopamine Neurotransmitter Release Cycle;Acetylcholine Neurotransmitter Release Cycle;GABA synthesis, release, reuptake and degradation;Neurotransmitter release cycle;Transmission across Chemical Synapses;Serotonin Neurotransmitter Release Cycle;Norepinephrine Neurotransmitter Release Cycle
(Consensus)
Intolerance Scores
- loftool
- rvis_EVS
- -0.16
- rvis_percentile_EVS
- 41.25
Haploinsufficiency Scores
- pHI
- hipred
- Y
- hipred_score
- 0.793
- ghis
- 0.630
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.731
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Cplx1
- Phenotype
- hearing/vestibular/ear phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); reproductive system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); cellular phenotype; growth/size/body region phenotype;
Gene ontology
- Biological process
- exocytosis;chemical synaptic transmission;synaptic vesicle exocytosis;regulation of exocytosis;insulin secretion;regulation of synaptic vesicle fusion to presynaptic active zone membrane;regulation of neurotransmitter secretion;exocytic insertion of neurotransmitter receptor to postsynaptic membrane
- Cellular component
- cytosol;dendrite;SNARE complex;neuronal cell body;terminal bouton;calyx of Held;synaptobrevin 2-SNAP-25-syntaxin-1a-complexin I complex;synaptobrevin 2-SNAP-25-syntaxin-3-complexin complex;Schaffer collateral - CA1 synapse;postsynapse;glutamatergic synapse
- Molecular function
- SNARE binding;neurotransmitter transporter activity;protein binding;syntaxin-1 binding