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GeneE
10 sources retrieved Β· Most recent: April 2026 Β· Index updated 14 days ago
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SLC38A3
solute carrier family 38 member 3
Chromosome 3 Β· 3p21.31
NCBI Gene: 10991Ensembl: ENSG00000188338.16HGNC: HGNC:18044UniProt: Q99624
33PubMed Papers
21Diseases
0Drugs
7Pathogenic Variants
FUNCTIONAL ROLE
Transporter
CLINICAL
OMIM Disease Gene
DATA QUALITY
βœ“ Experimental GO Evidenceβœ“ Swiss-Prot Reviewed
L-histidine transmembrane transporter activityL-alanine transmembrane transporter activityL-asparagine transmembrane transporter activityL-glutamine transmembrane transporter activitydevelopmental and epileptic encephalopathy 102neurodegenerative diseaseEpileptic encephalopathyundetermined early-onset epileptic encephalopathy
✦AI Summary

SLC38A3 encodes SNAT3, a sodium-coupled neutral amino acid transporter that functions as a symporter cotransporting glutamine, histidine, and asparagine with sodium ions while antiporting protons 1. In the central nervous system, SLC38A3 plays a critical role in the glutamate-GABA-glutamine cycle by transporting L-glutamine from astrocytes to neurons, supporting neurotransmitter synthesis 2. The transport mechanism is electroneutral, pH-dependent, and bidirectional depending on substrate concentration gradients 1. Biallelic SLC38A3 variants cause developmental and epileptic encephalopathy 102, characterized by global developmental delay, intellectual disability, hypotonia, drug-resistant epilepsy, and microcephaly 2. Metabolomic analysis in affected individuals revealed perturbations in glutamate, histidine, and nitrogen metabolism, indicating disease pathophysiology involves glutamine homeostasis disruption 2. Beyond neurological roles, SLC38A3 expression is dysregulated in multiple cancers. In breast cancer, particularly triple-negative breast cancer, SLC38A3 overexpression promotes metastasis via the GSK3Ξ²/Ξ²-catenin/EMT pathway while reducing oxidative stress 3. In hepatocellular carcinoma, SLC38A3 levels decrease relative to other glutamine transporters, and this decrease predicts worse survival outcomes 4. Conversely, in endometrial cancer, SLC38A3 functions as an oncogene with elevated expression 5. The DEAF1 transcription factor regulates SLC38A3 expression in HCC, promoting glutamine uptake and reducing ROS levels 6.

Sources cited
1
SLC38A3 functions as a sodium-coupled symporter of glutamine, histidine, and asparagine with proton antiport activity; transport is pH-dependent, saturable, and electroneutral
PMID: 10823827
2
Biallelic SLC38A3 variants cause developmental and epileptic encephalopathy with global developmental delay, intellectual disability, hypotonia, epilepsy, and microcephaly; metabolomic perturbations in glutamate, histidine, and nitrogen metabolism observed
PMID: 34605855
3
SLC38A3 is overexpressed in breast cancer, particularly TNBC; promotes metastasis via GSK3Ξ²/Ξ²-catenin/EMT pathway; reduces oxidative stress
PMID: 38309615
4
SLC38A3 levels decrease in hepatocellular carcinoma compared to normal liver; decreased SLC38A3 predicts worse survival outcomes
PMID: 39062801
5
SLC38A3 is identified as a key prognostic gene and oncogene in endometrial cancer with elevated expression in tumor samples
PMID: 39773448
6
DEAF1 transcription factor regulates SLC38A3 expression in hepatocellular carcinoma, promoting glutamine uptake and reducing ROS levels
PMID: 40554679
Disease Associationsβ“˜21
developmental and epileptic encephalopathy 102Open Targets
0.68Moderate
neurodegenerative diseaseOpen Targets
0.54Moderate
Epileptic encephalopathyOpen Targets
0.37Weak
undetermined early-onset epileptic encephalopathyOpen Targets
0.37Weak
neuroinflammatory disorderOpen Targets
0.34Weak
genetic disorderOpen Targets
0.19Weak
metabolic diseaseOpen Targets
0.17Weak
smoking behaviorOpen Targets
0.17Weak
Short statureOpen Targets
0.15Weak
hyperlipidemiaOpen Targets
0.13Weak
response to stimulusOpen Targets
0.08Suggestive
esophageal squamous cell carcinomaOpen Targets
0.08Suggestive
trauma complicationOpen Targets
0.08Suggestive
MenorrhagiaOpen Targets
0.07Suggestive
OligomenorrheaOpen Targets
0.07Suggestive
PolymenorrheaOpen Targets
0.06Suggestive
Abnormality of the skeletal systemOpen Targets
0.05Suggestive
cannabis dependenceOpen Targets
0.05Suggestive
generalised epilepsyOpen Targets
0.05Suggestive
smoking initiationOpen Targets
0.05Suggestive
Developmental and epileptic encephalopathy 102UniProt
Pathogenic Variants7
NM_006841.6(SLC38A3):c.1212G>A (p.Trp404Ter)Likely pathogenic
not provided|Developmental and epileptic encephalopathy 102
β˜…β˜†β˜†β˜†2025β†’ Residue 404
NM_006841.6(SLC38A3):c.856_859delPathogenic
Developmental and epileptic encephalopathy 102
β˜…β˜†β˜†β˜†2025
NM_006841.6(SLC38A3):c.187G>T (p.Glu63Ter)Pathogenic
Developmental and epileptic encephalopathy 102
β˜…β˜†β˜†β˜†2023β†’ Residue 63
NM_006841.6(SLC38A3):c.1123A>C (p.Thr375Pro)Pathogenic
Developmental and epileptic encephalopathy 102
β˜†β˜†β˜†β˜†2022β†’ Residue 375
NM_006841.6(SLC38A3):c.1119del (p.Val373_Leu374insTer)Pathogenic
Developmental and epileptic encephalopathy 102
β˜†β˜†β˜†β˜†2022β†’ Residue 373
NM_006841.6(SLC38A3):c.855+1G>TPathogenic
Developmental and epileptic encephalopathy 102
β˜†β˜†β˜†β˜†2022
NM_006841.6(SLC38A3):c.1049C>A (p.Ser350Ter)Pathogenic
Developmental and epileptic encephalopathy 102
β˜†β˜†β˜†β˜†2022β†’ Residue 350
View on ClinVar β†—
Related Genes
SCN11AProtein interaction77%SLC1A3Protein interaction76%SLC32A1Protein interaction76%SLC38A5Protein interaction69%SLC38A1Shared pathway38%SLC1A5Shared pathway31%
Tissue Expression6 tissues
Liver
100%
Heart
3%
Brain
2%
Ovary
2%
Lung
0%
Bone Marrow
0%
Gene Interaction Network
Click a node to explore
SLC38A3SCN11ASLC1A3SLC32A1SLC38A5SLC38A1SLC1A5
PROTEIN STRUCTURE
Preparing viewer…
AlphaFoldAI-predicted Β· UniProt Q99624
View on AlphaFold β†—
Constraintβ“˜
LOEUFβ“˜
0.43Moderately Constrained
pLIβ“˜
1.00Intolerant
Observed/Expected LoF0.28 [0.19–0.43]
RankingsWhere SLC38A3 stands among ~20K protein-coding genes
  • #11,415of 20,598
    Most Researched33
  • #3,245of 5,498
    Most Pathogenic Variants7
  • #2,340of 17,882
    Most Constrained (LOEUF)0.43 Β· top quartile
Genes detectedSLC38A3
Sources retrieved10 papers
Response timeβ€”
πŸ“„ Sources
10β–Ό
1
Glutamine transporter SLC38A3 promotes breast cancer metastasis via Gsk3Ξ²/Ξ²-catenin/EMT pathway.
PMID: 38309615
Cancer Lett Β· 2024
1.00
2
Regulation and function of the SLC38A3/SNAT3 glutamine transporter.
PMID: 27362266
Channels (Austin) Β· 2016
0.90
3
Reprogramming of Glutamine Amino Acid Transporters Expression and Prognostic Significance in Hepatocellular Carcinoma.
PMID: 39062801
Int J Mol Sci Β· 2024
0.80
4
Down regulation of 3p genes, LTF, SLC38A3 and DRR1, upon growth of human chromosome 3-mouse fibrosarcoma hybrids in severe combined immunodeficiency mice.
PMID: 16432833
Int J Cancer Β· 2006
0.70
5
Identification and validation of glucose metabolism-related gene signature in endometrial cancer.
PMID: 39773448
BMC Cancer Β· 2025
0.60