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

Gene ID: 6509, updated on 15-Apr-2019

Summary

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
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

Genomic context

See SLC1A4 in Genome Data Viewer
Location:
2p14
Exon count:
9
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 2 NC_000002.12 (64988445..65023865)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (65215579..65250999)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107985888 Neighboring gene uncharacterized LOC107984063 Neighboring gene ribosomal protein L11 pseudogene 1 Neighboring gene RNA, U6 small nuclear 548, pseudogene Neighboring gene long intergenic non-protein coding RNA 2576 Neighboring gene centrosomal protein 68 Neighboring gene RAB1A, member RAS oncogene family

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Spastic tetraplegia, thin corpus callosum, and progressive microcephaly
MedGen: C4225254 OMIM: 616657 GeneReviews: Not available
Compare labs

NHGRI GWAS Catalog

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

Pathways from BioSystems

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Process Evidence Code Pubs
L-alanine transport IDA
Inferred from Direct Assay
more info
PubMed 
L-cystine transport IDA
Inferred from Direct Assay
more info
PubMed 
NOT L-cystine transport IDA
Inferred from Direct Assay
more info
PubMed 
L-serine transport IDA
Inferred from Direct Assay
more info
PubMed 
amino acid transport TAS
Traceable Author Statement
more info
 
chloride transmembrane transport IEA
Inferred from Electronic Annotation
more info
 
cognition IMP
Inferred from Mutant Phenotype
more info
PubMed 
glutamine transport TAS
Traceable Author Statement
more info
PubMed 
hydroxyproline transport IDA
Inferred from Direct Assay
more info
PubMed 
proline transmembrane transport IEA
Inferred from Electronic Annotation
more info
 
proline transport IDA
Inferred from Direct Assay
more info
PubMed 
synaptic transmission, glutamatergic NAS
Non-traceable Author Statement
more info
PubMed 
threonine transport IDA
Inferred from Direct Assay
more info
PubMed 
Component Evidence Code Pubs
cell surface HDA PubMed 
centrosome IDA
Inferred from Direct Assay
more info
 
dendrite IEA
Inferred from Electronic Annotation
more info
 
extracellular exosome HDA PubMed 
integral component of membrane NAS
Non-traceable Author Statement
more info
PubMed 
integral component of plasma membrane IC
Inferred by Curator
more info
PubMed 
intermediate filament ISS
Inferred from Sequence or Structural Similarity
more info
 
melanosome IEA
Inferred from Electronic Annotation
more info
 
membrane HDA PubMed 
microtubule organizing center IDA
Inferred from Direct Assay
more info
 
neuronal cell body IEA
Inferred from Electronic Annotation
more info
 
plasma membrane TAS
Traceable Author Statement
more info
 

General protein information

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)

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
    5917..40421
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

    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:2179
    SDF; Sodium:dicarboxylate symporter family
  2. NM_001348406.1NP_001335335.1  neutral amino acid transporter A isoform 3 precursor

    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:2257
    SDF; Sodium:dicarboxylate symporter family
  3. NM_001348407.1NP_001335336.1  neutral amino acid transporter A isoform 3 precursor

    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:2257
    SDF; Sodium:dicarboxylate symporter family
  4. NM_003038.5NP_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
    P43007
    Related
    ENSP00000234256.3, ENST00000234256.4
    Conserved Domains (1) summary
    pfam00375
    Location:72477
    SDF; Sodium:dicarboxylate symporter family

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000002.12 Reference GRCh38.p12 Primary Assembly

    Range
    64988445..65023865
    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.
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