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

Summary

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, Dec 2024]
Expression: Biased expression in liver (RPKM 98.6) and brain (RPKM 9.7) See more
Orthologs: mouse all
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Genomic context

Location:: 3p21.31

Exon count:: 16

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	3	NC_000003.12 (50205271..50221486)
RS_2024_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_000003.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
Biallelic variants in SLC38A3 encoding a glutamine transporter cause epileptic encephalopathy.
Title: Biallelic variants in SLC38A3 encoding a glutamine transporter cause epileptic encephalopathy.
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.
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.
SNAT3 is expressed in the placenta in the early stage of pregnancy.
Title: Expression and role of SNAT3 in the placenta.
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.
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.
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.

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Phenotypes

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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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

PMC22669P16 (e-PCR)
- UniSTS:272128

RH65839 (e-PCR)
- UniSTS:13327

STS-T62038 (e-PCR)
- UniSTS:24610

RH75882 (e-PCR)
- UniSTS:89988

D3S3181 (e-PCR)
- UniSTS:153506

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, 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, 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, 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	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	ISS Inferred from Sequence or Structural Similarity more info
involved_in L-glutamine import across plasma membrane	ISS Inferred from Sequence or Structural Similarity more info
involved_in L-histidine import across plasma membrane	ISS Inferred from Sequence or Structural Similarity 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 transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in asparagine transport	IDA Inferred from Direct Assay more info	PubMed
involved_in cellular response to potassium ion starvation	IEA Inferred from Electronic Annotation more info
involved_in female pregnancy	IEA Inferred from Electronic Annotation more info
involved_in glutamine secretion	ISS Inferred from Sequence or Structural Similarity more info
involved_in glutamine transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in glutamine transport	IDA Inferred from Direct Assay more info	PubMed
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	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 positive regulation of transcription by RNA polymerase II	IEA Inferred from Electronic Annotation more info
involved_in sodium ion 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	ISS Inferred from Sequence or Structural Similarity more info
located_in basolateral plasma 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	ISS Inferred from Sequence or Structural Similarity more info
located_in plasma membrane	TAS Traceable Author Statement more info

General protein information

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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

NCBI Reference Sequences (RefSeq)

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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)

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_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000003.12 Reference GRCh38.p14 Primary Assembly

Range

50205271..50221486

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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