CLSTN3
Basic information
Region (hg38): 12:7129698-7158945
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (124 variants)
- not_provided (8 variants)
- Autism_spectrum_disorder (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the CLSTN3 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000014718.4. 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 | 5 | |||||
| missense | 124 | 126 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 124 | 5 | 2 |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| CLSTN3 | protein_coding | protein_coding | ENST00000266546 | 18 | 29248 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.970 | 0.0298 | 125730 | 0 | 16 | 125746 | 0.0000636 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.50 | 487 | 589 | 0.826 | 0.0000366 | 6244 |
| Missense in Polyphen | 75 | 130.35 | 0.57539 | 1478 | ||
| Synonymous | -0.166 | 246 | 243 | 1.01 | 0.0000155 | 1910 |
| Loss of Function | 4.98 | 7 | 41.7 | 0.168 | 0.00000195 | 481 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000152 | 0.000152 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000218 | 0.000217 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000803 | 0.0000791 |
| Middle Eastern | 0.000218 | 0.000217 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: May modulate calcium-mediated postsynaptic signals. Complex formation with APBA2 and APP, stabilizes APP metabolism and enhances APBA2-mediated suppression of beta-APP40 secretion, due to the retardation of intracellular APP maturation. {ECO:0000250}.;
Recessive Scores
- pRec
- 0.103
Intolerance Scores
- loftool
- 0.364
- rvis_EVS
- -1.65
- rvis_percentile_EVS
- 2.76
Haploinsufficiency Scores
- pHI
- 0.359
- hipred
- Y
- hipred_score
- 0.654
- ghis
- 0.621
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.293
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Clstn3
- Phenotype
- behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); 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); skeleton phenotype; growth/size/body region phenotype;
Gene ontology
- Biological process
- regulation of cell growth;homophilic cell adhesion via plasma membrane adhesion molecules;synapse assembly;synaptic transmission, glutamatergic;positive regulation of synaptic transmission;synaptic transmission, GABAergic;positive regulation of synapse assembly;positive regulation of protein localization to synapse;regulation of presynapse assembly
- Cellular component
- Golgi membrane;endoplasmic reticulum membrane;cell surface;protein-containing complex;postsynaptic membrane;glutamatergic synapse;GABA-ergic synapse;integral component of postsynaptic density membrane
- Molecular function
- calcium ion binding