SLC8A3

protein-coding

solute carrier family 8 member A3, the group of Solute carrier family 8

Gene summary

This gene encodes a member of the sodium/calcium exchanger integral membrane protein family. Na+/Ca2+ exchange proteins are involved in maintaining Ca2+ homeostasis in a wide variety of cell types. The protein is regulated by intracellular calcium ions and is found in both the plasma membrane and intracellular organellar membranes, where exchange of Na+ for Ca2+ occurs in an electrogenic manner. Alternative splicing has been observed for this gene and multiple variants have been described. [provided by RefSeq, Aug 2013]

MANE transcript

NM_182932.3

Inheritance

—

ClinVar variants

U:125B:10

Top phenotype

Prostate cancer

gnomAD constraint

pLI —, LoF o/e 0.36

Max pathogenic AF

—

Genomic locus

chr14:70,044,215-70,189,480

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~145.3 kb
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GenCC 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 SLC8A3 variants in ClinVar

4 Conditions Cataloged
not specifiedTotal: 121
not providedTotal: 11
Prostate cancerTotal: 1
Malignant hyperthermia, susceptibility to, 1Total: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_182932.3. 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.

EffectPLPVUSLBBSum
synonymous
3
clinvar
4
clinvar
7
missense
123
clinvar
1
clinvar
2
clinvar
126
nonsense
1
clinvar
1
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
1
clinvar
1
Total0012546135
Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 38 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_182932.3RefSeqNP_891977.16MANE Select
ENST00000356921.7EnsemblENSP00000349392.36MANE Select
NM_001130417.3RefSeqNP_001123889.15Standard
NM_001438068.1RefSeqNP_001424997.16Standard

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

  • hematopoietic progenitor cell differentiation
  • ion transport
  • mitochondrial calcium ion transmembrane transport
  • cellular calcium ion homeostasis
  • cell communication

Molecular Function

  • calcium:sodium antiporter activity
  • calmodulin binding
  • metal ion binding
  • ion antiporter activity involved in regulation of postsynaptic membrane potential

Cellular Component

  • mitochondrial outer membrane
  • endoplasmic reticulum membrane
  • microtubule
  • plasma membrane
  • integral component of plasma membrane

gnomAD Constraint

Source: gnomAD

Gene type
protein_coding
Transcript type
protein_coding
Transcript
ENST00000381269
Coding exons
7
Length
144854
Individuals with no LoFs
125728
Homozygous LoFs
0
Heterozygous LoFs
20
Defined
125748
p
0.0000795
Z-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense0.4175085350.9490.00002936106
Missense (PolyPhen)181219.140.825962431
Synonymous-0.1082112091.010.00001191874
Loss of Function3.301130.80.3580.00000172353

Population LoF Frequency

PopulationCAFp-valueStatus
African00.0absent
Latino/Admixed American0.000140.00014rare
Ashkenazi Jewish0.0000990.000099rare
East Asian0.0000550.000054rare
Finnish00.0absent
European (Non-Finnish)0.000110.00011rare
South Asian00.0absent
Other0.000160.00016rare

dbNSFP Gene Annotations

Source: dbNSFP

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, both in muscle and in brain. In a first phase, voltage-gated channels mediate the rapid increase of cytoplasmic Ca(2+) levels due to release of Ca(2+) stores from the endoplasmic reticulum. SLC8A3 mediates the export of Ca(2+) from the cell during the next phase, so that cytoplasmic Ca(2+) levels rapidly return to baseline. Contributes to Ca(2+) transport during excitation-contraction coupling in muscle. In neurons, 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 (By similarity). Required for normal oligodendrocyte differentiation and for normal myelination (PubMed:21959935). Mediates Ca(2+) efflux from mitochondria and contributes to mitochondrial Ca(2+) ion homeostasis (By similarity). {ECO:0000250|UniProtKB:S4R2P9, ECO:0000269|PubMed:21959935}.;

Recessive Scores

pRec
0.157

Intolerance Scores

LoFtool
0.388
RVIS EVS
-1.06
RVIS percentile EVS
7.55

Essentials

Essential (CRISPR)
N
Essential (CRISPR2)
N
Essential (gene trap)
N
Indispensability pred.
N
Indispensability score
0.311

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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