SLC8A2
solute carrier family 8 member A2, the group of Solute carrier family 8
Basic information
Region (hg38): 19:47428017-47471893
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (65 variants)
- not_provided (8 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC8A2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000015063.3. 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 | 9 | |||||
| missense | 63 | 64 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 63 | 9 | 1 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| SLC8A2 | protein_coding | protein_coding | ENST00000236877 | 9 | 44152 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.996 | 0.00367 | 125743 | 0 | 5 | 125748 | 0.0000199 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 5.24 | 224 | 579 | 0.387 | 0.0000353 | 5898 |
| Missense in Polyphen | 49 | 234.98 | 0.20853 | 2308 | ||
| Synonymous | 1.51 | 236 | 267 | 0.882 | 0.0000191 | 1943 |
| Loss of Function | 4.55 | 3 | 29.8 | 0.101 | 0.00000136 | 334 |
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 | 0.0000663 | 0.0000462 |
| European (Non-Finnish) | 0.0000266 | 0.0000264 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000327 | 0.0000327 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Mediates the electrogenic exchange of Ca(2+) against Na(+) ions across the cell membrane, and thereby contributes to the regulation of cytoplasmic Ca(2+) levels and Ca(2+)-dependent cellular processes. Contributes to cellular Ca(2+) homeostasis in excitable cells. Contributes to the rapid decrease of cytoplasmic Ca(2+) levels back to baseline after neuronal activation, and thereby contributes to modulate synaptic plasticity, learning and memory. Plays a role in regulating urinary Ca(2+) and Na(+) excretion. {ECO:0000250|UniProtKB:Q8K596}.;
- Pathway
- Protein digestion and absorption - Homo sapiens (human);Calcium signaling pathway - Homo sapiens (human);Apelin signaling pathway - Homo sapiens (human);cGMP-PKG signaling pathway - Homo sapiens (human);Olfactory transduction - Homo sapiens (human);Antiarrhythmic Pathway, Pharmacodynamics;Ion homeostasis;Sodium/Calcium exchangers;Transport of inorganic cations/anions and amino acids/oligopeptides;SLC-mediated transmembrane transport;Transport of small molecules;Cardiac conduction;Muscle contraction;Hemostasis;Reduction of cytosolic Ca++ levels;Platelet calcium homeostasis;Platelet homeostasis
(Consensus)
Recessive Scores
- pRec
- 0.142
Intolerance Scores
- loftool
- 0.0166
- rvis_EVS
- -1
- rvis_percentile_EVS
- 8.32
Haploinsufficiency Scores
- pHI
- 0.317
- hipred
- hipred_score
- ghis
- 0.647
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.451
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Slc8a2
- 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);
Gene ontology
- Biological process
- ion transport;cellular calcium ion homeostasis;cell communication;learning;memory;sodium ion transmembrane transport;regulation of short-term neuronal synaptic plasticity;long-term synaptic potentiation;calcium ion transmembrane transport;regulation of cardiac conduction
- Cellular component
- plasma membrane;integral component of plasma membrane;basolateral plasma membrane;dendritic spine;perikaryon
- Molecular function
- calcium:sodium antiporter activity;calmodulin binding;metal ion binding