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SLC1A4 solute carrier family 1 member 4 [ Homo sapiens (human) ]

Gene ID: 6509, updated on 5-Mar-2024

Summary

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Official Symbol
SLC1A4provided by HGNC
Official Full Name
solute carrier family 1 member 4provided by HGNC
Primary source
HGNC:HGNC:10942
See related
Ensembl:ENSG00000115902 MIM:600229; AllianceGenome:HGNC:10942
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
SATT; ASCT1; SPATCCM
Summary
The protein encoded by this gene is a sodium-dependent neutral amino acid transporter for alanine, serine, cysteine, and threonine. Defects in this gene have been associated with developmental delay, microcephaly, and intellectual disability. [provided by RefSeq, Jan 2017]
Expression
Broad expression in brain (RPKM 33.8), adrenal (RPKM 12.8) and 23 other tissues See more
Orthologs
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Genomic context

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Location:
2p14
Exon count:
9
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (64988479..65023865)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (64998100..65033490)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (65215613..65250999)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene small nucleolar RNA U13 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15912 Neighboring gene long intergenic non-protein coding RNA 2245 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15913 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15914 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15915 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15916 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15919 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15918 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15917 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:65165275-65165830 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15920 Neighboring gene ribosomal protein L11 pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15921 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15922 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11570 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:65216535-65217119 Neighboring gene RNA, U6 small nuclear 548, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15923 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr2:65258211-65259074 Neighboring gene long intergenic non-protein coding RNA 2576 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15924 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:65277603-65277775 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15925 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11573 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11572 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11574 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11575 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:65288315-65288816 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:65294702-65295470 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:65295471-65296237 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:65297006-65297772 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr2:65304333-65305043 Neighboring gene centrosomal protein 68 Neighboring gene RAB1A, member RAS oncogene family

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. A rare cause of microcephaly, thin corpus callosum and refractory epilepsy due to a novel SLC1A4 gene mutation. Sarigecili E, et al. Clin Neurol Neurosurg, 2022 Jul. PMID 35605507
  2. Novel European SLC1A4 variant: infantile spasms and population ancestry analysis. Conroy J, et al. J Hum Genet, 2016 Aug. PMID 27193218
  3. SLC1A4 mutations cause a novel disorder of intellectual disability, progressive microcephaly, spasticity and thin corpus callosum. Heimer G, et al. Clin Genet, 2015 Oct. PMID 26138499
  4. A homozygous mutation in SLC1A4 in siblings with severe intellectual disability and microcephaly. Srour M, et al. Clin Genet, 2015 Jul. PMID 25930971
  5. Na+ interactions with the neutral amino acid transporter ASCT1. Scopelliti AJ, et al. J Biol Chem, 2014 Jun 20. PMID 24808181, Free PMC Article

See all (61) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. A rare cause of microcephaly, thin corpus callosum and refractory epilepsy due to a novel SLC1A4 gene mutation.
    Title: A rare cause of microcephaly, thin corpus callosum and refractory epilepsy due to a novel SLC1A4 gene mutation.
  2. Results suggest that ASCT1/2 may play an important role in regulating extracellular d-serine and NMDA receptor-mediated physiological effects and that ASCT1/2 inhibitors have the potential for therapeutic benefit.
    Title: Phenylglycine analogs are inhibitors of the neutral amino acid transporters ASCT1 and ASCT2 and enhance NMDA receptor-mediated LTP in rat visual cortex slices.
  3. ANKRD50 simultaneously engages multiple parts of the SNX27-retromer-WASH complex machinery in a direct and co-operative interaction network that is needed to efficiently recycle the nutrient transporters
    Title: Retromer- and WASH-dependent sorting of nutrient transporters requires a multivalent interaction network with ANKRD50.
  4. SLC1A4 deficiency should not be considered a population-specific disorder, and all patients with unexplained severe neurodevelopmental delay and the features outlined should be investigated regardless of ethnicity, as there are no known metabolic markers of this potentially treatable condition.
    Title: Novel European SLC1A4 variant: infantile spasms and population ancestry analysis.
  5. SLC1A4 is the disease causing gene of a novel neurologic disorder manifesting with significant intellectual disability, severe postnatal microcephaly, spasticity and thin corpus callosum.
    Title: SLC1A4 mutations cause a novel disorder of intellectual disability, progressive microcephaly, spasticity and thin corpus callosum.
  6. ASCT1 is essential in brain serine transport.
    Title: Mutations in SLC1A4, encoding the brain serine transporter, are associated with developmental delay, microcephaly and hypomyelination.
  7. SLC1A4 disruption may impair brain development and function by decreasing the levels of L-serine in neurons. The identification of additional families with mutations in SLC1A4 would be necessary to confirm its involvement in intellectual disability.
    Title: A homozygous mutation in SLC1A4 in siblings with severe intellectual disability and microcephaly.
  8. Na+ interactions with the neutral amino acid transporter ASCT1.
    Title: Na+ interactions with the neutral amino acid transporter ASCT1.
  9. This study revealed genetic associations of SLC1A4, SQSTM1, and EIF4EBP1 with MSA. These results may lend genetic support to the hypothesis that oxidative stress is associated with the pathogenesis of MSA.
    Title: Associations between multiple system atrophy and polymorphisms of SLC1A4, SQSTM1, and EIF4EBP1 genes.
  10. SLC1A4 gene is associated with schizophrenia.
    Title: Association study of polymorphisms in the neutral amino acid transporter genes SLC1A4, SLC1A5 and the glycine transporter genes SLC6A5, SLC6A9 with schizophrenia.
Submit: New GeneRIF Correction See all GeneRIFs (14)

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
Spastic tetraplegia-thin corpus callosum-progressive postnatal microcephaly syndrome
MedGen: C4225254 OMIM: 616657 GeneReviews: Not available
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EBI GWAS Catalog

Description
An atlas of genetic influences on human blood metabolites.
EBI GWAS Catalog
Genome-wide association study identifies multiple loci influencing human serum metabolite levels.
EBI GWAS Catalog
Novel Loci for metabolic networks and multi-tissue expression studies reveal genes for atherosclerosis.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

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

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables L-alanine transmembrane transporter activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables L-alanine transmembrane transporter activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables L-alanine transmembrane transporter activity IMP
Inferred from Mutant Phenotype
more info
 PubMed 
enables L-aspartate transmembrane transporter activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables L-aspartate transmembrane transporter activity ISS
Inferred from Sequence or Structural Similarity
more info
  
NOT enables L-cystine transmembrane transporter activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables L-cystine transmembrane transporter activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables L-glutamine transmembrane transporter activity TAS
Traceable Author Statement
more info
 PubMed 
enables L-hydroxyproline transmembrane transporter activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables L-proline transmembrane transporter activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables L-serine transmembrane transporter activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables L-serine transmembrane transporter activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables L-serine transmembrane transporter activity IMP
Inferred from Mutant Phenotype
more info
 PubMed 
enables L-threonine transmembrane transporter activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables L-threonine transmembrane transporter activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables amino acid transmembrane transporter activity TAS
Traceable Author Statement
more info
  
enables chloride channel activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables symporter activity IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in L-alanine import across plasma membrane IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in L-alanine transport IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in L-aspartate import across plasma membrane ISS
Inferred from Sequence or Structural Similarity
more info
  
NOT involved_in L-cystine transport IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in L-cystine transport IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in L-glutamate transmembrane transport IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in L-serine import across plasma membrane IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in L-serine transport IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in L-serine transport IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in amino acid transport TAS
Traceable Author Statement
more info
  
involved_in chloride transmembrane transport IEA
Inferred from Electronic Annotation
more info
  
involved_in cognition IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in glutamine transport TAS
Traceable Author Statement
more info
 PubMed 
involved_in hydroxyproline transport IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in proline transmembrane transport IEA
Inferred from Electronic Annotation
more info
  
involved_in proline transport IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in synaptic transmission, glutamatergic NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in threonine transport IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in transport across blood-brain barrier NAS
Non-traceable Author Statement
more info
 PubMed 
Component Evidence Code Pubs
located_in cell surface HDA PubMed 
located_in centrosome IDA
Inferred from Direct Assay
more info
  
located_in extracellular exosome HDA PubMed 
located_in intermediate filament ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in melanosome IEA
Inferred from Electronic Annotation
more info
  
located_in membrane HDA PubMed 
located_in membrane IDA
Inferred from Direct Assay
more info
 PubMed 
located_in membrane NAS
Non-traceable Author Statement
more info
 PubMed 
is_active_in plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in plasma membrane IC
Inferred by Curator
more info
 PubMed 
is_active_in plasma membrane IMP
Inferred from Mutant Phenotype
more info
 PubMed 
located_in plasma membrane TAS
Traceable Author Statement
more info
  
located_in synapse IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
neutral amino acid transporter A
Names
alanine/serine/cysteine/threonine transporter 1
glutamate/neutral amino acid transporter
solute carrier family 1 (glutamate/neutral amino acid transporter), member 4

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.

Genomic

  1. NG_053002.1 RefSeqGene

    Range
    5955..40421
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001193493.2 → NP_001180422.1  neutral amino acid transporter A isoform 2

    See identical proteins and their annotated locations for NP_001180422.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR and coding sequence and lacks an alternate in-frame exon compared to variant 1. The resulting isoform (2) is shorter at the N-terminus and lacks an alternate internal segment compared to isoform 1.
    Source sequence(s)
    AK295687, BC026216, BC072423, DA218921
    Consensus CDS
    CCDS54362.1
    UniProtKB/Swiss-Prot
    P43007
    Related
    ENSP00000431942.1, ENST00000531327.5
    Conserved Domains (1) summary
    cl00573
    Location:2 → 179
    SDF; Sodium:dicarboxylate symporter family

  2. NM_001348406.2 → NP_001335335.1  neutral amino acid transporter A isoform 3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (3) is shorter at the N-terminus compared to isoform 1. Variants 3 and 4 both encode the same isoform (3).
    Source sequence(s)
    AC007386
    Conserved Domains (1) summary
    pfam00375
    Location:2 → 257
    SDF; Sodium:dicarboxylate symporter family

  3. NM_001348407.2 → NP_001335336.1  neutral amino acid transporter A isoform 3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (3) is shorter at the N-terminus compared to isoform 1. Variants 3 and 4 both encode the same isoform (3).
    Source sequence(s)
    AC007386
    Conserved Domains (1) summary
    pfam00375
    Location:2 → 257
    SDF; Sodium:dicarboxylate symporter family

  4. NM_003038.5 → NP_003029.2  neutral amino acid transporter A isoform 1

    See identical proteins and their annotated locations for NP_003029.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    BC026216, BC072423, CR990382, L19444
    Consensus CDS
    CCDS1879.1
    UniProtKB/Swiss-Prot
    B7Z3C0, D6W5F0, P43007
    UniProtKB/TrEMBL
    B2R7N6
    Related
    ENSP00000234256.3, ENST00000234256.4
    Conserved Domains (1) summary
    pfam00375
    Location:72 → 477
    SDF; Sodium:dicarboxylate symporter family

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    64988479..65023865
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    64998100..65033490
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_001135581.1: Suppressed sequence

    Description
    NM_001135581.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P43007.1 GenPept UniProtKB/Swiss-Prot:P43007

Gene LinkOut

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