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GARS1 glycyl-tRNA synthetase 1 [ Homo sapiens (human) ]

Gene ID: 2617, updated on 3-Nov-2024

Summary

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Official Symbol
GARS1provided by HGNC
Official Full Name
glycyl-tRNA synthetase 1provided by HGNC
Primary source
HGNC:HGNC:4162
See related
Ensembl:ENSG00000106105 MIM:600287; AllianceGenome:HGNC:4162
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
GARS; HMN5; CMT2D; DSMAV; GlyRS; HMN5A; HMND5; SMAD1; SMAJI
Summary
This gene encodes glycyl-tRNA synthetase, one of the aminoacyl-tRNA synthetases that charge tRNAs with their cognate amino acids. The encoded enzyme is an (alpha)2 dimer which belongs to the class II family of tRNA synthetases. It has been shown to be a target of autoantibodies in the human autoimmune diseases, polymyositis or dermatomyositis. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2015]
Expression
Ubiquitous expression in thyroid (RPKM 31.7), testis (RPKM 29.9) and 25 other tissues See more
Orthologs
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Genomic context

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See GARS1 in Genome Data Viewer
Location:
7p14.3
Exon count:
17
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (30594735..30634033)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (30732340..30771637)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (30634351..30673649)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr7:30588305-30588806 Neighboring gene TRPC6 pseudogene 10 Neighboring gene GARS1 divergent transcript Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25815 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:30633949-30634562 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:30634563-30635176 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:30635177-30635790 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:30681423-30682118 Neighboring gene uncharacterized LOC124901609 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:30692507-30693496 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr7:30694345-30695544 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:30701754-30702296 Neighboring gene corticotropin releasing hormone receptor 2 Neighboring gene MPRA-validated peak6463 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18070 Neighboring gene uncharacterized LOC124901608

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 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?
  1. Multiple omics integrative analysis identifies GARS1 as a novel prognostic and immunological biomarker: from pan-cancer to bladder cancer.
    Title: Multiple omics integrative analysis identifies GARS1 as a novel prognostic and immunological biomarker: from pan-cancer to bladder cancer.
  2. Glycyl-tRNA Synthetase Induces Psoriasis-Like Skin by Facilitating Skin Inflammation and Vascular Endothelial Cell Angiogenesis.
    Title: Glycyl-tRNA Synthetase Induces Psoriasis-Like Skin by Facilitating Skin Inflammation and Vascular Endothelial Cell Angiogenesis.
  3. Glycyl-tRNA Synthetase (GARS) Expression Is Associated with Prostate Cancer Progression and Its Inhibition Decreases Migration, and Invasion In Vitro.
    Title: Glycyl-tRNA Synthetase (GARS) Expression Is Associated with Prostate Cancer Progression and Its Inhibition Decreases Migration, and Invasion In Vitro.
  4. Pathogenic missense variants altering codon 336 of GARS1 lead to divergent dominant phenotypes.
    Title: Pathogenic missense variants altering codon 336 of GARS1 lead to divergent dominant phenotypes.
  5. Two distinct receptor-binding domains of human glycyl-tRNA synthetase 1 displayed on extracellular vesicles activate M1 polarization and phagocytic bridging of macrophages to cancer cells.
    Title: Two distinct receptor-binding domains of human glycyl-tRNA synthetase 1 displayed on extracellular vesicles activate M1 polarization and phagocytic bridging of macrophages to cancer cells.
  6. GARS is implicated in poor survival and immune infiltration of hepatocellular carcinoma.
    Title: GARS is implicated in poor survival and immune infiltration of hepatocellular carcinoma.
  7. Charcot-Marie-Tooth mutation in glycyl-tRNA synthetase stalls ribosomes in a pre-accommodation state and activates integrated stress response.
    Title: Charcot-Marie-Tooth mutation in glycyl-tRNA synthetase stalls ribosomes in a pre-accommodation state and activates integrated stress response.
  8. Associations between Neurological Diseases and Mutations in the Human Glycyl-tRNA Synthetase.
    Title: Associations between Neurological Diseases and Mutations in the Human Glycyl-tRNA Synthetase.
  9. GARS-related disease in infantile spinal muscular atrophy: Implications for diagnosis and treatment.
    Title: GARS-related disease in infantile spinal muscular atrophy: Implications for diagnosis and treatment.
  10. Clinical and Genetic Features in a Series of Eight Unrelated Patients with Neuropathy Due to Glycyl-tRNA Synthetase (GARS) Variants.
    Title: Clinical and Genetic Features in a Series of Eight Unrelated Patients with Neuropathy Due to Glycyl-tRNA Synthetase (GARS) Variants.
Submit: New GeneRIF Correction See all GeneRIFs (44)

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 Variation Viewer (GRCh37.p13)

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 ATP binding IEA
Inferred from Electronic Annotation
more info
  
enables ATP:ATP adenylyltransferase activity IEA
Inferred from Electronic Annotation
more info
  
enables bis(5'-nucleosyl)-tetraphosphatase (asymmetrical) activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables glycine-tRNA ligase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables glycine-tRNA ligase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables glycine-tRNA ligase activity IMP
Inferred from Mutant Phenotype
more info
 PubMed 
enables identical protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein dimerization activity IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
involved_in diadenosine tetraphosphate biosynthetic process IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in mitochondrial glycyl-tRNA aminoacylation IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in tRNA aminoacylation for protein translation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
located_in axon IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in cytosol IDA
Inferred from Direct Assay
more info
  
located_in cytosol TAS
Traceable Author Statement
more info
  
located_in extracellular exosome ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in mitochondrial matrix TAS
Traceable Author Statement
more info
  
located_in mitochondrion HTP PubMed 
is_active_in mitochondrion IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in secretory granule IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
glycine--tRNA ligase
Names
AP-4-A synthetase
Charcot-Marie-Tooth neuropathy 2D
Charcot-Marie-Tooth neuropathy, neuronal type, D
ap4A synthetase
diadenosine tetraphosphate synthetase
NP_001303701.1
NP_002038.2

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_007942.1 RefSeqGene

    Range
    5001..44469
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_243

mRNA and Protein(s)

  1. NM_001316772.1 → NP_001303701.1  glycine--tRNA ligase isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an upstream transcription start site compared to variant 1. This variant contains a uORF that was shown in PMID: 26327585 to block translation from the same start codon used in variant 1. Therefore, this variant uses a downstream translation initiation site compared to variant 1 and encodes an isoform (2) that is shorter at the N-terminus compared to isoform 1.
    Source sequence(s)
    AA464978, AC005154, BC007755, DA386636
    UniProtKB/TrEMBL
    A0A6Q8PGA8
    Related
    ENSP00000502174.1, ENST00000675693.1
    Conserved Domains (4) summary
    PLN02734
    Location:7 → 670
    PLN02734; glycyl-tRNA synthetase
    cd00774
    Location:70 → 416
    GlyRS-like_core; Glycyl-tRNA synthetase (GlyRS)-like class II core catalytic domain. GlyRS functions as a homodimer in eukaryotes, archaea and some bacteria and as a heterotetramer in the remainder of prokaryotes. It is responsible for the attachment of glycine to the 3' ...
    cd00858
    Location:534 → 657
    GlyRS_anticodon; GlyRS Glycyl-anticodon binding domain. GlyRS belongs to class II aminoacyl-tRNA synthetases (aaRS). This alignment contains the anticodon binding domain, which is responsible for specificity in tRNA-binding, so that the activated amino acid is ...
    cd00935
    Location:10 → 60
    GlyRS_RNA; GlyRS_RNA binding domain. This short RNA-binding domain is found at the N-terminus of GlyRS in several higher eukaryote aminoacyl-tRNA synthetases (aaRSs). This domain consists of a helix-turn-helix structure , which is similar to other RNA-binding ...

  2. NM_002047.4 → NP_002038.2  glycine--tRNA ligase isoform 1 precursor

    See identical proteins and their annotated locations for NP_002038.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longer isoform (1).
    Source sequence(s)
    AA464978, AC005154, BC007755, DA386636
    Consensus CDS
    CCDS43564.1
    UniProtKB/Swiss-Prot
    A0A090N8G0, B3KQA2, B4DIA0, P41250, Q969Y1
    UniProtKB/TrEMBL
    A0A6Q8PGZ8
    Related
    ENSP00000373918.3, ENST00000389266.8
    Conserved Domains (1) summary
    PLN02734
    Location:61 → 724
    PLN02734; glycyl-tRNA synthetase

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_000007.14 Reference GRCh38.p14 Primary Assembly

    Range
    30594735..30634033
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    30732340..30771637
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P41250.3 GenPept UniProtKB/Swiss-Prot:P41250

Gene LinkOut

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