SLC5A3
protein-codingsolute carrier family 5 member 3, the group of Solute carrier family 5
Gene summary
Enables myo-inositol:sodium symporter activity; potassium channel regulator activity; and transmembrane transporter binding activity. Predicted to be involved in monosaccharide transmembrane transport and myo-inositol import across plasma membrane. Predicted to act upstream of or within several processes, including inositol metabolic process; positive regulation of reactive oxygen species biosynthetic process; and regulation of respiratory gaseous exchange. Located in perinuclear region of cytoplasm and plasma membrane. [provided by Alliance of Genome Resources, Jun 2026]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~32.7 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 SLC5A3 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_006933.7. 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 | 1 | 1 | ||||
| missense | 40 | 40 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 40 | 1 | 0 | 41 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_008864.4 | 1 | MANE Select | |
| Ensembl | ENSP00000370543.3 | 1 | MANE Select | |
| Ensembl | ENSP00000811203.1 | 1 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Nuclear Receptors Meta-Pathway
- NRF2 pathway
- Inositol transporters
- Transport of bile salts and organic acids, metal ions and amine compounds
- SLC-mediated transmembrane transport
Biological Process
- inositol metabolic process
- sodium ion transport
- peripheral nervous system development
- myo-inositol transport
- regulation of respiratory gaseous exchange
Molecular Function
- myo-inositol:sodium symporter activity
- glucose:sodium symporter activity
Cellular Component
- plasma membrane
- integral component of plasma membrane
- integral component of membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000381151
- Coding exons
- 1
- Length
- 32690
- Individuals with no LoFs
- 125723
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 12
- Defined
- 125735
- p
- 0.0000477
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 2.76 | 247 | 403 | 0.613 | 0.0000211 | 4708 |
| Missense (PolyPhen) | 31 | 144.62 | 0.21435 | 1637 | ||
| Synonymous | -1.55 | 172 | 148 | 1.16 | 0.00000792 | 1472 |
| Loss of Function | 3.66 | 2 | 19.4 | 0.103 | 9.78e-7 | 243 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00012 | 0.00012 | rare |
| Latino/Admixed American | 0.000029 | 0.000029 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00011 | 0.00011 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000053 | 0.000053 | rare |
| South Asian | 0.000033 | 0.000033 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Prevents intracellular accumulation of high concentrations of myo-inositol (an osmolyte) that result in impairment of cellular function.;
Recessive Scores
- pRec
- 0.381
Intolerance Scores
- LoFtool
- 0.0843
- RVIS EVS
- -0.67
- RVIS percentile EVS
- 15.86
Essentials
- Essential (CRISPR)
- E
- Essential (CRISPR2)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.114
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |