SLC38A3

Chr 3

solute carrier family 38 member 3

Also known as: DEE102, G17, NAT1, SN1, SNAT3

NCBI Gene: 10991 ENSG00000188338 UniProt: Q99624

The SLC38A3 protein is a sodium-coupled amino acid transporter that cotransports glutamine, histidine, and asparagine across cell membranes and plays a critical role in the glutamate-GABA-glutamine cycle in the brain by facilitating glutamine uptake into neurons for neurotransmitter synthesis. Biallelic mutations cause developmental and epileptic encephalopathy 102, an autosomal recessive disorder affecting brain development and causing seizures. This condition primarily impacts the central nervous system through disruption of amino acid transport essential for normal neurotransmitter metabolism.

ResearchSummary from RefSeq, OMIM, UniProt

Enables L-amino acid transmembrane transporter activity. Involved in carboxylic acid transport. Located in plasma membrane. Implicated in developmental and epileptic encephalopathy 102. [provided by Alliance of Genome Resources, Jul 2025]

ResearchGenerating clinical summary…

LOFmechanism

Clinical Summary— SLC38A3

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ClinVar Variants

7 unique Pathogenic / Likely Pathogenic· 56 VUS of 72 total submissions

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Some data sources returned errors (1)

omim: Error: OMIM fetch failed: 429

Population Genetics & Constraint

gnomAD

Constraint data not available from gnomAD.

Curated Mechanism (G2P)Gene2Phenotype (DDG2P) ↗

strongSLC38A3-related epileptic encephalopathyLOFAR

This gene — mechanism propensity

Predictions shown for reference only — model trained on dominant genes, not applicable to AR conditions.

0.6162th %ile

GOF

0.73top 25%

LOF

0.3647th %ile

The Badonyi & Marsh prediction model was trained exclusively on dominant disease genes. Predictions are not reliable for genes with autosomal recessive inheritance and are shown at reduced opacity for reference only.

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.

ClinVar Variant Classifications

72 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic6

Likely Pathogenic1

VUS56

Likely Benign3

Pathogenic

Likely Pathogenic

VUS

Likely Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

Classification	LoF	Missense + Inframe	Non-coding	Total
Pathogenic	5	1	0	6
Likely Pathogenic	1	0	0	1
VUS	0	55	1	56
Likely Benign	0	3	0	3
Benign	0	0	0	0
Total	6	59	1	66

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

10 pathogenic / likely-pathogenic (of 12) ClinVar copy-number / structural variants overlap SLC38A3 — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →