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

Summary

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: mouse all
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Genomic context

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_000007.14 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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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?

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.
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.
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.
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.
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.
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.
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.
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.
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.
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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Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Charcot-Marie-Tooth disease type 2D MedGen: C1832274 OMIM: 601472 GeneReviews: GARS-Associated Axonal Neuropathy, Charcot-Marie-Tooth Hereditary Neuropathy Overview	not available
Neuronopathy, distal hereditary motor, type 5A MedGen: CN031873 OMIM: 600794 GeneReviews: GARS-Associated Axonal Neuropathy, BSCL2-Related Neurologic Disorders / Seipinopathy, Charcot-Marie-Tooth Hereditary Neuropathy Overview	not available
Spinal muscular atrophy, infantile, James type MedGen: C5436669 OMIM: 619042 GeneReviews: GARS-Associated Axonal Neuropathy	not available

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

D7S1808 (e-PCR)
- UniSTS:25378

SHGC-31691 (e-PCR)
- UniSTS:59459

D7S2049E (e-PCR)
- UniSTS:151112

BARC0022 (e-PCR)
- UniSTS:255308

GARS (e-PCR)
- UniSTS:503631

RH47187 (e-PCR)
- UniSTS:9306

RH47185 (e-PCR)
- UniSTS:43417

D7S435 (e-PCR), detects polymorphism
- UniSTS:76188

D7S2836 (e-PCR)
- UniSTS:3558

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 more info	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

EC 6.1.1.14

NP_002038.2

EC 6.1.1.14

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_007942.1 RefSeqGene

Range

5001..44469

Download

GenBank, FASTA, Sequence Viewer (Graphics), LRG_243

mRNA and Protein(s)

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 ...
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