SLC8A2
protein-codingsolute carrier family 8 member A2, the group of Solute carrier family 8
Gene summary
Predicted to enable calcium:monoatomic cation antiporter activity involved in regulation of postsynaptic cytosolic calcium ion concentration and calcium:sodium antiporter activity. Predicted to be involved in several processes, including learning or memory; monoatomic cation transmembrane transport; and regulation of short-term neuronal synaptic plasticity. Predicted to act upstream of or within several processes, including modulation of chemical synaptic transmission; regulation of action potential firing pattern; and response to ischemia. Located in presynapse. Biomarker of Alzheimer's disease. [provided by Alliance of Genome Resources, Jul 2025]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~43.9 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 SLC8A2 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_015063.3. 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 | 4 | 8 | 1 | 13 | ||
| missense | 83 | 1 | 84 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 87 | 9 | 1 | 97 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_055878.1 | 9 | MANE Select | |
| Ensembl | ENSP00000236877.5 | 9 | MANE Select | |
| Ensembl | ENSP00000437536.1 | 8 | Standard | |
| Ensembl | ENSP00000437536.1 | 8 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- 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)
Biological Process
- ion transport
- cellular calcium ion homeostasis
- cell communication
- learning
- memory
Molecular Function
- calcium:sodium antiporter activity
- calmodulin binding
- metal ion binding
Cellular Component
- plasma membrane
- integral component of plasma membrane
- basolateral plasma membrane
- dendritic spine
- perikaryon
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000236877
- Coding exons
- 9
- Length
- 44152
- Individuals with no LoFs
- 125743
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 5
- Defined
- 125748
- p
- 0.0000199
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 5.24 | 224 | 579 | 0.387 | 0.0000353 | 5898 |
| Missense (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 |
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 | 0.000066 | 0.000046 | rare |
| European (Non-Finnish) | 0.000027 | 0.000026 | rare |
| South Asian | 0.000033 | 0.000033 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
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}.;
Recessive Scores
- pRec
- 0.142
Intolerance Scores
- LoFtool
- 0.0166
- RVIS EVS
- -1
- RVIS percentile EVS
- 8.32
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.451
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |