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SLC38A4 solute carrier family 38 member 4 [ Homo sapiens (human) ]

Gene ID: 55089, updated on 10-Dec-2024

Summary

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Official Symbol
SLC38A4provided by HGNC
Official Full Name
solute carrier family 38 member 4provided by HGNC
Primary source
HGNC:HGNC:14679
See related
Ensembl:ENSG00000139209 MIM:608065; AllianceGenome:HGNC:14679
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
ATA3; NAT3; PAAT; SNAT4
Summary
SLC38A4 is found predominantly in liver and transports both cationic and neutral amino acids. The transport of cationic amino acids by SLC38A4 is Na(+) and pH independent, while the transport of neutral amino acids is Na(+) and pH dependent (Hatanaka et al., 2001 [PubMed 11342143]).[supplied by OMIM, Mar 2008]
Expression
Restricted expression toward liver (RPKM 138.1) See more
Orthologs
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Genomic context

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See SLC38A4 in Genome Data Viewer
Location:
12q13.11
Exon count:
18
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (46764761..46832431, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (46724005..46791701, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (47158544..47219780, complement)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene SLC38A4 antisense RNA 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:46997992-46998511 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:47011695-47012195 Neighboring gene olfactory receptor family 7 subfamily A member 19 pseudogene Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:47063431-47064104 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:47064118-47064618 Neighboring gene microtubule affinity regulating kinase 3 pseudogene 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:47219240-47219798 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:47219799-47220356 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:47225315-47226123 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:47232393-47232579 Neighboring gene uncharacterized LOC124902924 Neighboring gene uncharacterized LOC124902925

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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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Related articles in PubMed

  1. The SNAT4 isoform of the system A amino acid transporter is functional in human placental microvillous plasma membrane. Desforges M, et al. J Physiol, 2009 Jan 15. PMID 19015196, Free PMC Article
  2. Evidence for the transport of neutral as well as cationic amino acids by ATA3, a novel and liver-specific subtype of amino acid transport system A. Hatanaka T, et al. Biochim Biophys Acta, 2001 Feb 9. PMID 11342143
  3. A novel human amino acid transporter, hNAT3: cDNA cloning, chromosomal mapping, genomic structure, expression, and functional characterization. Gu S, et al. Genomics, 2001 Jun 15. PMID 11414754
  4. Sodium-coupled neutral amino acid (System N/A) transporters of the SLC38 gene family. Mackenzie B, et al. Pflugers Arch, 2004 Feb. PMID 12845534
  5. SNAT4 isoform of system A amino acid transporter is expressed in human placenta. Desforges M, et al. Am J Physiol Cell Physiol, 2006 Jan. PMID 16148032

See all (24) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Platelets Affect the Activity of Amino Acid Transporter SNAT4 in HuH-7 Human Hepatoma Cells.
    Title: Platelets Affect the Activity of Amino Acid Transporter SNAT4 in HuH-7 Human Hepatoma Cells.
  2. SLC38A4 Amino Acid Transporter Expression Is Significantly Lower in Early Preterm Intrauterine Growth Restriction Complicated Placentas.
    Title: SLC38A4 Amino Acid Transporter Expression Is Significantly Lower in Early Preterm Intrauterine Growth Restriction Complicated Placentas.
  3. SLC38A4 functions as a tumour suppressor in hepatocellular carcinoma through modulating Wnt/beta-catenin/MYC/HMGCS2 axis.
    Title: SLC38A4 functions as a tumour suppressor in hepatocellular carcinoma through modulating Wnt/β-catenin/MYC/HMGCS2 axis.
  4. three SNPs (corepressor interacting with RBPJ 1 (CIR1) rs13009079T>C, ribonucleotide reductase M1 (RRM1) rs1465952T>C and solute carrier family 38, member 4 (SLC38A4) rs2429467C>T), may play a role in the pathogenesis of lung cancer
    Title: Polymorphisms in cancer-related pathway genes and lung cancer.
  5. PAAT is a novel ATPase and a trans-regulator of mitochondrial ABC transporters that plays an important role in the maintenance of mitochondrial homeostasis
    Title: PAAT, a novel ATPase and trans-regulator of mitochondrial ABC transporters, is critically involved in the maintenance of mitochondrial homeostasis.
  6. Our results suggest that mutant allele A for SNP 1304 G>A of SLC38A4 gene is associated with hyperglycaemia.
    Title: Association of the polymorphisms 292 C>T and 1304 G>A in the SLC38A4 gene with hyperglycaemia.
  7. Membrane topological structure of neutral system N/A amino acid transporter 4 (SNAT4) protein
    Title: Membrane topological structure of neutral system N/A amino acid transporter 4 (SNAT4) protein.
  8. Report SNAT4 activity in fetal T lymphocytes in intrauterine growth restriction and with tumor necrosis factor-alpha treatment.
    Title: Amino acid transport systems beta and A in fetal T lymphocytes in intrauterine growth restriction and with tumor necrosis factor-alpha treatment.
  9. the contribution of SNAT4 to system A-mediated placental microvillous transport decreases between first trimester and term
    Title: The SNAT4 isoform of the system A amino acid transporter is functional in human placental microvillous plasma membrane.
  10. evidence of SNAT4 mRNA and protein expression in the human placenta, both at the first trimester and at full term
    Title: SNAT4 isoform of system A amino acid transporter is expressed in human placenta.
Submit: New GeneRIF Correction

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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ10191, MGC126876

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables L-amino acid transmembrane transporter activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables L-arginine transmembrane transporter activity IEA
Inferred from Electronic Annotation
more info
  
enables alanine:sodium symporter activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables amino acid transmembrane transporter activity TAS
Traceable Author Statement
more info
  
enables amino acid:sodium symporter activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables neutral L-amino acid:sodium symporter activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in L-alanine import across plasma membrane IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in L-arginine transmembrane transport IEA
Inferred from Electronic Annotation
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 neutral amino acid transport IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in sodium ion transmembrane transport IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in microvillus membrane IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in plasma membrane IBA
Inferred from Biological aspect of Ancestor
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 4
Names
N amino acid transporter 3
Na(+)-coupled neutral amino acid transporter 4
amino acid transporter A3
amino acid transporter system A3
system A amino acid transporter 3
system N amino acid transporter 3

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)

  1. NM_001143824.2 → NP_001137296.1  sodium-coupled neutral amino acid transporter 4

    See identical proteins and their annotated locations for NP_001137296.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1 and 2 both encode the same protein.
    Source sequence(s)
    AC008014, AC080136, KF459548
    Consensus CDS
    CCDS8750.1
    UniProtKB/Swiss-Prot
    A8K553, Q969I6
    Related
    ENSP00000389843.1, ENST00000447411.5
    Conserved Domains (2) summary
    COG0814
    Location:71 → 534
    SdaC; Amino acid permease [Amino acid transport and metabolism]
    cl00456
    Location:73 → 535
    SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain

  2. NM_018018.5 → NP_060488.2  sodium-coupled neutral amino acid transporter 4

    See identical proteins and their annotated locations for NP_060488.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longer transcript. Variants 1 and 2 both encode the same protein.
    Source sequence(s)
    AC008014, AC080136, KF459548
    Consensus CDS
    CCDS8750.1
    UniProtKB/Swiss-Prot
    A8K553, Q969I6
    Related
    ENSP00000266579.4, ENST00000266579.9
    Conserved Domains (2) summary
    COG0814
    Location:71 → 534
    SdaC; Amino acid permease [Amino acid transport and metabolism]
    cl00456
    Location:73 → 535
    SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain

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

  1. NC_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    46764761..46832431 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005268997.3 → XP_005269054.1  sodium-coupled neutral amino acid transporter 4 isoform X1

    See identical proteins and their annotated locations for XP_005269054.1

    UniProtKB/Swiss-Prot
    A8K553, Q969I6
    Conserved Domains (2) summary
    COG0814
    Location:71 → 534
    SdaC; Amino acid permease [Amino acid transport and metabolism]
    cl00456
    Location:73 → 535
    SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    46724005..46791701 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054372383.1 → XP_054228358.1  sodium-coupled neutral amino acid transporter 4 isoform X1

    UniProtKB/Swiss-Prot
    A8K553, Q969I6

  2. XM_054372385.1 → XP_054228360.1  sodium-coupled neutral amino acid transporter 4 isoform X1

    UniProtKB/Swiss-Prot
    A8K553, Q969I6

  3. XM_054372384.1 → XP_054228359.1  sodium-coupled neutral amino acid transporter 4 isoform X1

    UniProtKB/Swiss-Prot
    A8K553, Q969I6
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q969I6.1 GenPept UniProtKB/Swiss-Prot:Q969I6

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