CPLX3
Basic information
Region (hg38): 15:74826627-74831802
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the CPLX3 gene is commonly pathogenic or not.
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.
| Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 14 | 14 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 14 | 0 | 0 |
Variants in CPLX3
This is a list of pathogenic ClinVar variants found in the CPLX3 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 15-74826734-G-A | not specified | Uncertain significance (Jan 18, 2022) | ||
| 15-74826818-A-G | not specified | Uncertain significance (Nov 17, 2022) | ||
| 15-74828041-C-T | not specified | Uncertain significance (Dec 20, 2024) | ||
| 15-74828045-A-G | not specified | Uncertain significance (Feb 08, 2025) | ||
| 15-74828074-C-T | not specified | Uncertain significance (Jun 24, 2022) | ||
| 15-74828080-A-G | not specified | Uncertain significance (Jan 19, 2024) | ||
| 15-74828099-G-A | not specified | Uncertain significance (May 05, 2023) | ||
| 15-74828108-A-G | not specified | Uncertain significance (Feb 28, 2023) | ||
| 15-74830131-A-G | not specified | Uncertain significance (Jan 06, 2023) | ||
| 15-74830152-T-C | not specified | Uncertain significance (Mar 17, 2023) | ||
| 15-74830169-G-A | not specified | Uncertain significance (Jan 24, 2024) | ||
| 15-74830171-C-A | not specified | Uncertain significance (Jan 01, 2025) | ||
| 15-74830172-G-A | not specified | Uncertain significance (May 24, 2024) | ||
| 15-74830181-C-A | not specified | Uncertain significance (Feb 23, 2023) | ||
| 15-74830263-T-G | not specified | Uncertain significance (Oct 27, 2022) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| CPLX3 | protein_coding | protein_coding | ENST00000395018 | 3 | 5254 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.240 | 0.731 | 125683 | 0 | 13 | 125696 | 0.0000517 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.513 | 81 | 95.1 | 0.852 | 0.00000541 | 1025 |
| Missense in 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 |
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) | 0.00000943 | 0.00000880 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.000393 | 0.000359 |
| Other | 0.000176 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: Positively regulates a late step in synaptic vesicle exocytosis. {ECO:0000250}.;
- Pathway
- Synaptic vesicle cycle - Homo sapiens (human);Synaptic Vesicle Pathway
(Consensus)
Intolerance Scores
- loftool
- 0.246
- rvis_EVS
- 0.01
- rvis_percentile_EVS
- 54.95
Haploinsufficiency Scores
- pHI
- 0.216
- hipred
- N
- hipred_score
- 0.380
- ghis
- 0.465
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.614
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Cplx3
- Phenotype
- 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); vision/eye 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);
Gene ontology
- Biological process
- synaptic vesicle exocytosis;insulin secretion;regulation of synaptic vesicle fusion to presynaptic active zone membrane;regulation of neurotransmitter secretion
- Cellular component
- cytosol;cell junction;SNARE complex;terminal bouton;photoreceptor ribbon synapse;anchored component of synaptic vesicle membrane;anchored component of presynaptic active zone membrane
- Molecular function
- SNARE binding;neurotransmitter transporter activity;syntaxin binding