U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

SLC38A3 solute carrier family 38 member 3 [ Homo sapiens (human) ]

Gene ID: 10991, updated on 3-Jun-2026
Official Symbol
SLC38A3provided by HGNC
Official Full Name
solute carrier family 38 member 3provided by HGNC
Primary source
HGNC:HGNC:18044
See related
Ensembl:ENSG00000188338 MIM:604437; AllianceGenome:HGNC:18044
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
G17; SN1; NAT1; SNAT3; DEE102
Summary
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]
Expression
Biased expression in liver (RPKM 98.6) and brain (RPKM 9.7) See more
Orthologs
all
Try the new Gene page
Try the new Transcripts and proteins table
See SLC38A3 in Genome Data Viewer
Location:
3p21.31
Exon count:
16
Annotation release Status Assembly Chr Location
RS_2025_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (50205271..50221486)
RS_2025_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (50234602..50250823)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (50242704..50258918)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene SEMA3F antisense RNA 1 Neighboring gene basic proline-rich protein-like Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14382 Neighboring gene Sharpr-MPRA regulatory region 10077 Neighboring gene semaphorin 3F Neighboring gene ReSE screen-validated silencer GRCh37_chr3:50207171-50207381 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:50207797-50208770 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:50230799-50231315 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:50231316-50231832 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:50231833-50232348 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:50232401-50232932 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14384 Neighboring gene G protein subunit alpha transducin 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:50246621-50247149 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:50250030-50250839 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_70487 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:50257474-50257974 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:50257975-50258475 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:50263389-50264198 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14385 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19890 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:50272293-50272903 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:50272904-50273514 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19891 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:50275957-50276566 Neighboring gene microRNA 5787 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14387 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19892 Neighboring gene G protein subunit alpha i2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:50280231-50280841 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:50280842-50281451 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:50283071-50283786 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:50283787-50284502 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14388 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:50297648-50298153 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:50298661-50299165 Neighboring gene long independently transcribed non-coding RNA 3143 Neighboring gene semaphorin 3B

Go to nucleotide: Graphics FASTA GenBank

  • Project title: Tissue-specific circular RNA induction during human fetal development
  • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
  • BioProject: PRJNA270632
  • Publication: PMID 26076956
  • Analysis date: Mon Apr 2 22:54:59 2018

Related articles in PubMed

  1. Biallelic variants in SLC38A3 encoding a glutamine transporter cause epileptic encephalopathy. Marafi D, et al. Brain, 2022 Apr 29. PMID 34605855, Free PMC Article
  2. Amino acid transporter SLC38A3 promotes metastasis of non-small cell lung cancer cells by activating PDK1. Wang Y, et al. Cancer Lett, 2017 May 1. PMID 28202352
  3. Increased expression of a glutamine transporter SNAT3 is a marker of malignant gliomas. Sidoryk M, et al. Neuroreport, 2004 Mar 22. PMID 15094455
  4. Glutamine transporter SLC38A3 promotes breast cancer metastasis via Gsk3β/β-catenin/EMT pathway. Tan Z, et al. Cancer Lett, 2024 Apr 1. PMID 38309615, Free PMC Article
  5. Molecular analysis of system N suggests novel physiological roles in nitrogen metabolism and synaptic transmission. Chaudhry FA, et al. Cell, 1999 Dec 23. PMID 10619430

See all (33) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Glutamine transporter SLC38A3 promotes breast cancer metastasis via Gsk3beta/beta-catenin/EMT pathway.
    Title: Glutamine transporter SLC38A3 promotes breast cancer metastasis via Gsk3β/β-catenin/EMT pathway.
  2. Biallelic variants in SLC38A3 encoding a glutamine transporter cause epileptic encephalopathy.
    Title: Biallelic variants in SLC38A3 encoding a glutamine transporter cause epileptic encephalopathy.
  3. SLC38A3 activated PDK1/AKT signaling and promoted metastasis of non-small cell lung cancer cells through regulating glutamine and histidine transport.
    Title: Amino acid transporter SLC38A3 promotes metastasis of non-small cell lung cancer cells by activating PDK1.
  4. The regulation of SNAT3 gene expression by extracellular pH involves post-transcriptional and transcriptional mechanisms, the latter being distinct from the mechanisms that control the tissue-specific expression of the gene.
    Title: Expression of glutamine transporter Slc38a3 (SNAT3) during acidosis is mediated by a different mechanism than tissue-specific expression.
  5. SNAT3 is expressed in the placenta in the early stage of pregnancy.
    Title: Expression and role of SNAT3 in the placenta.
  6. SN1 is a target for the ubiquitin ligase Nedd4-2, which is inactivated by the serum and glucocorticoid inducible kinase SGK1, its isoform SGK3, and protein kinase B.
    Title: Properties and regulation of glutamine transporter SN1 by protein kinases SGK and PKB.
  7. SNAT3 mRNA showed a 3-5 times stronger expression in gliomas than in metastases or control tissue, and was virtually absent from glioma cultures. Native glioblastoma immunostained positively with anti-SNAT3 antibody.
    Title: Increased expression of a glutamine transporter SNAT3 is a marker of malignant gliomas.
  8. Transcription of the SLC38A3 gene was impaired in all 5 RCC cell lines analyzed. Our data indicate this gene as a putative tumour suppressor gene.
    Title: Down regulation of 3p genes, LTF, SLC38A3 and DRR1, upon growth of human chromosome 3-mouse fibrosarcoma hybrids in severe combined immunodeficiency mice.
Submit: New GeneRIF Correction

Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description Tests
Developmental and epileptic encephalopathy 102
MedGen: C5676991 OMIM: 619881 GeneReviews: Not available
not available

See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

Products Interactant Other Gene Complex Source Pubs Description

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables L-alanine transmembrane transporter activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables L-asparagine transmembrane transporter activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables L-asparagine transmembrane transporter activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables L-asparagine transmembrane transporter activity IEA
Inferred from Electronic Annotation
more info
  
enables L-asparagine, sodium:proton antiporter activity EXP
Inferred from Experiment
more info
 PubMed 
enables L-asparagine, sodium:proton antiporter activity IEA
Inferred from Electronic Annotation
more info
  
enables L-asparagine, sodium:proton antiporter activity ISS
Inferred from Sequence or Structural Similarity
more info
  
enables L-glutamine transmembrane transporter activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables L-glutamine transmembrane transporter activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables L-glutamine transmembrane transporter activity IEA
Inferred from Electronic Annotation
more info
  
enables L-glutamine, sodium:proton antiporter activity EXP
Inferred from Experiment
more info
 PubMed 
enables L-glutamine, sodium:proton antiporter activity IEA
Inferred from Electronic Annotation
more info
  
enables L-glutamine, sodium:proton antiporter activity ISS
Inferred from Sequence or Structural Similarity
more info
  
enables L-histidine transmembrane transporter activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables L-histidine transmembrane transporter activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables L-histidine transmembrane transporter activity IEA
Inferred from Electronic Annotation
more info
  
enables L-histidine, sodium:proton antiporter activity IEA
Inferred from Electronic Annotation
more info
  
enables L-histidine, sodium:proton antiporter activity ISS
Inferred from Sequence or Structural Similarity
more info
  
enables amino acid transmembrane transporter activity TAS
Traceable Author Statement
more info
  
enables neutral L-amino acid:sodium symporter activity IEA
Inferred from Electronic Annotation
more info
  
enables neutral L-amino acid:sodium symporter activity ISS
Inferred from Sequence or Structural Similarity
more info
  
Process Evidence Code Pubs
involved_in L-alanine transport IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in L-asparagine import across plasma membrane IEA
Inferred from Electronic Annotation
more info
  
involved_in L-asparagine import across plasma membrane ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in L-glutamine import across plasma membrane IEA
Inferred from Electronic Annotation
more info
  
involved_in L-glutamine import across plasma membrane ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in L-glutamine secretion IEA
Inferred from Electronic Annotation
more info
  
involved_in L-glutamine secretion ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in L-glutamine transport IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in L-glutamine transport IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in L-glutamine transport IEA
Inferred from Electronic Annotation
more info
  
involved_in L-histidine import across plasma membrane IEA
Inferred from Electronic Annotation
more info
  
involved_in L-histidine import across plasma membrane ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in L-histidine transmembrane transport IEA
Inferred from Electronic Annotation
more info
  
involved_in L-histidine transport IEA
Inferred from Electronic Annotation
more info
  
involved_in L-histidine transport ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in amino acid transmembrane transport IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in amino acid transport TAS
Traceable Author Statement
more info
  
involved_in asparagine transmembrane transport IEA
Inferred from Electronic Annotation
more info
  
involved_in asparagine transport IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in asparagine transport IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in asparagine transport IEA
Inferred from Electronic Annotation
more info
  
involved_in female pregnancy IEA
Inferred from Electronic Annotation
more info
  
involved_in histidine transport IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in histidine transport IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in intracellular amino acid homeostasis IEA
Inferred from Electronic Annotation
more info
  
involved_in intracellular amino acid homeostasis ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in positive regulation of glutamine transport IEA
Inferred from Electronic Annotation
more info
  
involved_in transport across blood-brain barrier NAS
Non-traceable Author Statement
more info
 PubMed 
Component Evidence Code Pubs
located_in apical plasma membrane IEA
Inferred from Electronic Annotation
more info
  
located_in apical plasma membrane ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in basolateral plasma membrane IEA
Inferred from Electronic Annotation
more info
  
located_in basolateral plasma membrane ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in membrane IEA
Inferred from Electronic Annotation
more info
  
is_active_in plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in plasma membrane IDA
Inferred from Direct Assay
more info
  
located_in plasma membrane IEA
Inferred from Electronic Annotation
more info
  
located_in plasma membrane ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in plasma membrane TAS
Traceable Author Statement
more info
  
Preferred Names
sodium-coupled neutral amino acid transporter 3
Names
N-system amino acid transporter 1
Na(+)-coupled neutral amino acid transporter 3
system N amino acid transporter 1
system N1 Na+ and H+-coupled glutamine transporter

NEW Try the new Transcript table

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_006841.6 → NP_006832.1  sodium-coupled neutral amino acid transporter 3

    See identical proteins and their annotated locations for NP_006832.1

    Status: VALIDATED

    Source sequence(s)
    AC002077, BM662099, BP362985, BX537382
    Consensus CDS
    CCDS74940.1
    UniProtKB/Swiss-Prot
    B2R8Q0, Q6IB34, Q99624
    Related
    ENSP00000481301.1, ENST00000614032.5
    Conserved Domains (2) summary
    COG0814
    Location:64 → 486
    SdaC; Amino acid permease [Amino acid transport and metabolism]
    pfam01490
    Location:64 → 491
    Aa_trans; Transmembrane amino acid transporter protein

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2025_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    50205271..50221486
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006712954.4 → XP_006713017.1  sodium-coupled neutral amino acid transporter 3 isoform X1

    See identical proteins and their annotated locations for XP_006713017.1

    UniProtKB/Swiss-Prot
    B2R8Q0, Q6IB34, Q99624
    Conserved Domains (2) summary
    COG0814
    Location:64 → 486
    SdaC; Amino acid permease [Amino acid transport and metabolism]
    pfam01490
    Location:64 → 491
    Aa_trans; Transmembrane amino acid transporter protein

RNA

  1. XR_001739987.3 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    50234602..50250823
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054345052.1 → XP_054201027.1  sodium-coupled neutral amino acid transporter 3 isoform X1

    UniProtKB/Swiss-Prot
    B2R8Q0, Q6IB34, Q99624

RNA

  1. XR_008486638.1 RNA Sequence

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q99624.1 GenPept UniProtKB/Swiss-Prot:Q99624

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

Chemical Information
Molecular Biology Databases
Research Materials
Miscellaneous