SLC1A3 solute carrier family 1 member 3 [Homo sapiens (human)] - Gene

Summary

Official Symbol: SLC1A3provided by HGNC
Official Full Name: solute carrier family 1 member 3provided by HGNC
Primary source: HGNC:HGNC:10941
See related: Ensembl:ENSG00000079215 MIM:600111; AllianceGenome:HGNC:10941
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: EA6; EAAT1; GLAST; GLAST1
Summary: This gene encodes a member of a member of a high affinity glutamate transporter family. This gene functions in the termination of excitatory neurotransmission in central nervous system. Mutations are associated with episodic ataxia, Type 6. Alternative splicing results in multiple transcript variants.[provided by RefSeq, Feb 2014]
Expression: Biased expression in brain (RPKM 174.8) and fat (RPKM 10.9) See more
Orthologs: mouse all
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Genomic context

Location:: 5p13.2

Exon count:: 12

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	5	NC_000005.10 (36606606..36688334)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	5	NC_060929.1 (36856459..36938148)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	5	NC_000005.9 (36606708..36688436)

Chromosome 5 - NC_000005.10 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: 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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Identification of Polymorphisms in EAAT1 Glutamate Transporter Gene SLC1A3 Associated with Reduced Migraine Risk.
Title: Identification of Polymorphisms in EAAT1 Glutamate Transporter Gene SLC1A3 Associated with Reduced Migraine Risk.
Diminished motor neuron activity driven by abnormal astrocytic EAAT1 glutamate transporter activity in spinal muscular atrophy is not fully restored after lentiviral SMN delivery.
Title: Diminished motor neuron activity driven by abnormal astrocytic EAAT1 glutamate transporter activity in spinal muscular atrophy is not fully restored after lentiviral SMN delivery.
Ataxia-linked SLC1A3 mutations alter EAAT1 chloride channel activity and glial regulation of CNS function.
Title: Ataxia-linked SLC1A3 mutations alter EAAT1 chloride channel activity and glial regulation of CNS function.
Microscopic Characterization of the Chloride Permeation Pathway in the Human Excitatory Amino Acid Transporter 1 (EAAT1).
Title: Microscopic Characterization of the Chloride Permeation Pathway in the Human Excitatory Amino Acid Transporter 1 (EAAT1).
Functional consequences of SLC1A3 mutations associated with episodic ataxia 6.
Title: Functional consequences of SLC1A3 mutations associated with episodic ataxia 6.
Deficiency in MT5-MMP Supports Branching of Human iPSCs-Derived Neurons and Reduces Expression of GLAST/S100 in iPSCs-Derived Astrocytes.
Title: Deficiency in MT5-MMP Supports Branching of Human iPSCs-Derived Neurons and Reduces Expression of GLAST/S100 in iPSCs-Derived Astrocytes.
Research on the Relationship Between Schizophrenia and Excitatory Amino Acid Transporter 1 Gene Based on Nanogold Amplification Technology.
Title: Research on the Relationship Between Schizophrenia and Excitatory Amino Acid Transporter 1 Gene Based on Nanogold Amplification Technology.
Excitatory amino acid transporter (EAAT)1 and EAAT2 mRNA levels are altered in the prefrontal cortex of subjects with schizophrenia.
Title: Excitatory amino acid transporter (EAAT)1 and EAAT2 mRNA levels are altered in the prefrontal cortex of subjects with schizophrenia.
EAAT1 variants associated with glaucoma.
Title: EAAT1 variants associated with glaucoma.
This comprehensive review will discuss the regulatory mechanisms of GLAST/GLT-1, their association with neurological disorders, and the pharmacological agents which mediate their expression and function-{REVIEW}
Title: The role of astrocytic glutamate transporters GLT-1 and GLAST in neurological disorders: Potential targets for neurotherapeutics.

Submit: New GeneRIF Correction See all GeneRIFs (86)

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
Episodic ataxia type 6 MedGen: C2675211 OMIM: 612656 GeneReviews: Hereditary Ataxia Overview	Compare labs

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

RH69887 (e-PCR)
- UniSTS:52746

WI-19296 (e-PCR)
- UniSTS:30477

D5S1950 (e-PCR)
- UniSTS:473367

L28325 (e-PCR)
- UniSTS:29555

RH66388 (e-PCR)
- UniSTS:37031

SGC34127 (e-PCR)
- UniSTS:56490

PMC311006P7 (e-PCR)
- UniSTS:272834

RH68232 (e-PCR)
- UniSTS:31699

RH80751 (e-PCR)
- UniSTS:83671

SLC1A3_404 (e-PCR)
- UniSTS:277727

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables L-glutamate transmembrane transporter activity	IBA Inferred from Biological aspect of Ancestor more info
enables L-glutamate transmembrane transporter activity	IDA Inferred from Direct Assay more info	PubMed
enables glutamate binding	IEA Inferred from Electronic Annotation more info
enables glutamate:sodium symporter activity	IBA Inferred from Biological aspect of Ancestor more info
enables glutamate:sodium symporter activity	IDA Inferred from Direct Assay more info	PubMed
enables glutamate:sodium symporter activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables high-affinity L-glutamate transmembrane transporter activity	IDA Inferred from Direct Assay more info	PubMed
enables high-affinity L-glutamate transmembrane transporter activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables high-affinity L-glutamate transmembrane transporter activity	TAS Traceable Author Statement more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables neutral L-amino acid transmembrane transporter activity	IBA Inferred from Biological aspect of Ancestor more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in D-aspartate import across plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
involved_in D-aspartate import across plasma membrane	IDA Inferred from Direct Assay more info	PubMed
involved_in D-aspartate import across plasma membrane	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in L-aspartate import across plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
involved_in L-aspartate import across plasma membrane	IDA Inferred from Direct Assay more info	PubMed
involved_in L-aspartate import across plasma membrane	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in L-glutamate import	IDA Inferred from Direct Assay more info	PubMed
involved_in L-glutamate import across plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
involved_in L-glutamate import across plasma membrane	IDA Inferred from Direct Assay more info	PubMed
involved_in L-glutamate import across plasma membrane	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in L-glutamate transmembrane transport	IDA Inferred from Direct Assay more info	PubMed
involved_in auditory behavior	IEA Inferred from Electronic Annotation more info
involved_in cell morphogenesis involved in neuron differentiation	IEA Inferred from Electronic Annotation more info
involved_in cellular response to cocaine	IEA Inferred from Electronic Annotation more info
involved_in chemical synaptic transmission	TAS Traceable Author Statement more info	PubMed
involved_in chloride transmembrane transport	IDA Inferred from Direct Assay more info	PubMed
involved_in cranial nerve development	IEA Inferred from Electronic Annotation more info
involved_in gamma-aminobutyric acid biosynthetic process	IEA Inferred from Electronic Annotation more info
involved_in intracellular sodium ion homeostasis	IEA Inferred from Electronic Annotation more info
involved_in monoatomic ion transport	TAS Traceable Author Statement more info
involved_in neuromuscular process controlling balance	IEA Inferred from Electronic Annotation more info
involved_in neurotransmitter transport	TAS Traceable Author Statement more info
involved_in neurotransmitter uptake	TAS Traceable Author Statement more info	PubMed
involved_in neutral amino acid transport	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of synaptic transmission	IEA Inferred from Electronic Annotation more info
involved_in potassium ion transmembrane transport	IDA Inferred from Direct Assay more info	PubMed
involved_in response to antibiotic	IEA Inferred from Electronic Annotation more info
involved_in response to light stimulus	IEA Inferred from Electronic Annotation more info
involved_in response to wounding	IEA Inferred from Electronic Annotation more info
involved_in response to xenobiotic stimulus	IEA Inferred from Electronic Annotation more info
involved_in sensory perception of sound	IEA Inferred from Electronic Annotation more info
involved_in transepithelial transport	ISS Inferred from Sequence or Structural Similarity more info
involved_in transport across blood-brain barrier	ISS Inferred from Sequence or Structural Similarity more info
involved_in transport across blood-brain barrier	NAS Non-traceable Author Statement more info	PubMed

Component	Evidence Code	Pubs
located_in basal plasma membrane	ISS Inferred from Sequence or Structural Similarity more info
located_in cell surface	IEA Inferred from Electronic Annotation more info
located_in cytoplasmic vesicle	ISS Inferred from Sequence or Structural Similarity more info
located_in membrane	TAS Traceable Author Statement more info	PubMed
part_of membrane protein complex	ISS Inferred from Sequence or Structural Similarity more info
located_in neuron projection	ISS Inferred from Sequence or Structural Similarity more info
located_in neuronal cell body	ISS Inferred from Sequence or Structural Similarity more info
located_in perinuclear region of cytoplasm	ISS Inferred from Sequence or Structural Similarity more info
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in plasma membrane	IMP Inferred from Mutant Phenotype more info	PubMed
located_in plasma membrane	ISS Inferred from Sequence or Structural Similarity more info
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: excitatory amino acid transporter 1

Names: GLAST-1; glutamate/aspartate transporter 1; sodium-dependent glutamate/aspartate transporter 1; solute carrier family 1 (glial high affinity glutamate transporter), member 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.

Genomic

NG_015890.1 RefSeqGene

Range

5252..86980

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001166695.3 → NP_001160167.1 excitatory amino acid transporter 1 isoform 2

See identical proteins and their annotated locations for NP_001160167.1

Status: REVIEWED

Description

Transcript Variant: This variant (GLAST1b, PMID:16042756) lacks an alternate in-frame exon in the 3' coding region, compared to variant GLAST. The encoded protein (isoform 2) is shorter, compared to isoform 1.

Source sequence(s)

AC008957, AF070609, AY954110, BC037310, DC320625

Consensus CDS

CCDS54844.1

UniProtKB/TrEMBL

Q8N169

Related

ENSP00000506424.1, ENST00000680125.1

Conserved Domains (1) summary

pfam00375
Location:50 → 452

SDF; Sodium:dicarboxylate symporter family
NM_001166696.3 → NP_001160168.1 excitatory amino acid transporter 1 isoform 3

See identical proteins and their annotated locations for NP_001160168.1

Status: REVIEWED

Description

Transcript Variant: This variant (3) differs in the 3' UTR and has multiple coding differences compared to variant GLAST. The encoded protein (isoform 3) is shorter and has a distinct C-terminus compared to isoform 1.

Source sequence(s)

AC010631, BC022285, DC320625

Consensus CDS

CCDS93705.1

UniProtKB/TrEMBL

A0A7P0T7Q9, Q7Z5T0

Related

ENSP00000506048.1, ENST00000512374.1
NM_001289939.2 → NP_001276868.1 excitatory amino acid transporter 1 isoform 4

Status: REVIEWED

Description

Transcript Variant: This variant (GLAST1a) lacks an alternate in-frame exon in the 5' coding region, compared to variant GLAST. The encoded protein (isoform 4) is shorter, compared to isoform 1.

Source sequence(s)

AF070609, AK057823, AK293886, BC022285, BC037310, DC320625

Consensus CDS

CCDS78004.1

UniProtKB/TrEMBL

A0A087WT87, B4DF14

Related

ENSP00000506599.1, ENST00000681909.1

Conserved Domains (1) summary

pfam00375
Location:45 → 451

SDF; Sodium:dicarboxylate symporter family
NM_001289940.2 → NP_001276869.1 excitatory amino acid transporter 1 isoform 5

Status: REVIEWED

Description

Transcript Variant: This variant (GLAST1c, PMID:22026960) lacks two alternate in-frame exons in the coding region, compared to variant GLAST. The encoded protein (isoform 5) is shorter, compared to isoform 1.

Source sequence(s)

AC008957, AF070609, AK312304, BC037310

Consensus CDS

CCDS78003.1

UniProtKB/TrEMBL

A0A087X0U3

Related

ENSP00000483657.1, ENST00000612708.5

Conserved Domains (1) summary

pfam00375
Location:50 → 385

SDF; Sodium:dicarboxylate symporter family
NM_004172.5 → NP_004163.3 excitatory amino acid transporter 1 isoform 1

See identical proteins and their annotated locations for NP_004163.3

Status: REVIEWED

Description

Transcript Variant: This variant (GLAST) represents the longest transcript and encodes the longest protein (isoform 1).

Source sequence(s)

AF070609, AK057823, BC037310, D26443, DC320625

Consensus CDS

CCDS3919.1

UniProtKB/Swiss-Prot

B2R5T3, P43003, Q4JCQ8

UniProtKB/TrEMBL

Q8N169

Related

ENSP00000265113.4, ENST00000265113.9

Conserved Domains (1) summary

pfam00375
Location:50 → 497

SDF; Sodium:dicarboxylate symporter family

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_000005.10 Reference GRCh38.p14 Primary Assembly

Range

36606606..36688334

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_005248342.4 → XP_005248399.1 excitatory amino acid transporter 1 isoform X1

See identical proteins and their annotated locations for XP_005248399.1

UniProtKB/Swiss-Prot

B2R5T3, P43003, Q4JCQ8

UniProtKB/TrEMBL

Q8N169

Conserved Domains (1) summary

pfam00375
Location:50 → 497

SDF; Sodium:dicarboxylate symporter family
XM_047417539.1 → XP_047273495.1 excitatory amino acid transporter 1 isoform X2

UniProtKB/TrEMBL

Q8N169

Related

ENSP00000505850.1, ENST00000681926.1
XM_047417540.1 → XP_047273496.1 excitatory amino acid transporter 1 isoform X3

UniProtKB/TrEMBL

B4DF14

Alternate T2T-CHM13v2.0

Genomic

NC_060929.1 Alternate T2T-CHM13v2.0

Range

36856459..36938148

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054353189.1 → XP_054209164.1 excitatory amino acid transporter 1 isoform X1

UniProtKB/Swiss-Prot

B2R5T3, P43003, Q4JCQ8

UniProtKB/TrEMBL

Q8N169
XM_054353190.1 → XP_054209165.1 excitatory amino acid transporter 1 isoform X2

UniProtKB/TrEMBL

Q8N169
XM_054353191.1 → XP_054209166.1 excitatory amino acid transporter 1 isoform X3

UniProtKB/TrEMBL

B4DF14