Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene SNPs Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID Entrez Gene ID - the GENE ID in NCBI Gene database.	2617
Gene name Gene Name - the full gene name approved by the HGNC.	Glycyl-tRNA synthetase 1
Gene symbol Gene Symbol - the official gene symbol approved by the HGNC.	GARS1
Synonyms (NCBI Gene) Gene synonyms aliases	CMT2D, DSMAV, GARS, GlyRS, HMN5, HMN5A, HMND5, SMAD1, SMAJI
Chromosome Chromosome number	7
Chromosome location Chromosomal Location - indicates the cytogenetic location of the gene or region on the chromosome.	7p14.3
Summary Summary of gene provided in NCBI Entrez Gene.	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 t

Show/Hide all(32)

SNP ID	Visualize variation	Clinical significance	Consequence
rs77518956	G>A	Uncertain-significance, conflicting-interpretations-of-pathogenicity	Missense variant, coding sequence variant
rs137852643	G>C	Uncertain-significance, pathogenic, likely-pathogenic	Missense variant, coding sequence variant
rs137852644	T>C	Uncertain-significance, pathogenic	Missense variant, coding sequence variant
rs137852645	A>G	Uncertain-significance, pathogenic	Missense variant, coding sequence variant
rs137852646	G>A,C	Uncertain-significance, pathogenic	Missense variant, coding sequence variant
rs137852647	G>A	Uncertain-significance, pathogenic	Missense variant, coding sequence variant
rs137852648	C>T	Pathogenic	Missense variant, coding sequence variant
rs183573304	C>G,T	Conflicting-interpretations-of-pathogenicity	Coding sequence variant, synonymous variant
rs192443850	A>G	Likely-pathogenic, conflicting-interpretations-of-pathogenicity, uncertain-significance, likely-benign	Missense variant, coding sequence variant
rs200279483	A>G	Benign-likely-benign, conflicting-interpretations-of-pathogenicity	Synonymous variant, coding sequence variant
rs200887429	G>A,T	Conflicting-interpretations-of-pathogenicity, uncertain-significance, likely-benign	Missense variant, coding sequence variant, 5 prime UTR variant
rs201358272	C>G,T	Pathogenic, uncertain-significance, benign	Missense variant, coding sequence variant
rs370057212	C>A,T	Conflicting-interpretations-of-pathogenicity, uncertain-significance	Missense variant, coding sequence variant
rs370608239	G>A	Conflicting-interpretations-of-pathogenicity, likely-benign	Synonymous variant, coding sequence variant
rs376324026	G>A,C	Conflicting-interpretations-of-pathogenicity, likely-benign, benign, uncertain-significance	Intron variant
rs376772628	G>A	Conflicting-interpretations-of-pathogenicity, uncertain-significance	Missense variant, coding sequence variant
rs762624758	G>A	Likely-benign, conflicting-interpretations-of-pathogenicity	Synonymous variant, coding sequence variant, 5 prime UTR variant
rs797044855	G>A,C	Pathogenic, uncertain-significance	Coding sequence variant, missense variant
rs863224873	A>C,G,T	Uncertain-significance, likely-pathogenic	Coding sequence variant, missense variant
rs886043231	T>C	Conflicting-interpretations-of-pathogenicity	Synonymous variant, coding sequence variant
rs1057519166	C>T	Conflicting-interpretations-of-pathogenicity	5 prime UTR variant, coding sequence variant, synonymous variant
rs1060502838	A>G	Uncertain-significance, pathogenic	Missense variant, coding sequence variant
rs1060502839	G>A	Likely-pathogenic	Missense variant, coding sequence variant
rs1064795123	T>C,G	Pathogenic, likely-pathogenic	Missense variant, coding sequence variant
rs1135401747	AGAA>-	Pathogenic	5 prime UTR variant, coding sequence variant, frameshift variant
rs1135401748	G>A	Pathogenic	Missense variant, coding sequence variant
rs1554337974	C>T	Likely-pathogenic, uncertain-significance	Coding sequence variant, missense variant
rs1554338260	A>T	Pathogenic, uncertain-significance	Coding sequence variant, missense variant
rs1554338262	T>A	Pathogenic	Coding sequence variant, missense variant
rs1554338272	G>A	Pathogenic	Splice donor variant
rs1554340340	G>A	Pathogenic	Splice donor variant
rs1584026191	G>C	Likely-pathogenic	Coding sequence variant, missense variant

Show/Hide all(38)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000166	Function	Nucleotide binding	IEA
GO:0004081	Function	Bis(5'-nucleosyl)-tetraphosphatase (asymmetrical) activity	IDA	19710017
GO:0004812	Function	Aminoacyl-tRNA ligase activity	IEA
GO:0004820	Function	Glycine-tRNA ligase activity	IBA
GO:0004820	Function	Glycine-tRNA ligase activity	IDA	17544401, 17545306, 19710017
GO:0004820	Function	Glycine-tRNA ligase activity	IEA
GO:0004820	Function	Glycine-tRNA ligase activity	IMP	28675565
GO:0005515	Function	Protein binding	IPI	17545306, 17595294, 32814053
GO:0005524	Function	ATP binding	IEA
GO:0005576	Component	Extracellular region	IEA
GO:0005737	Component	Cytoplasm	IBA
GO:0005737	Component	Cytoplasm	IEA
GO:0005737	Component	Cytoplasm	TAS	7961834
GO:0005739	Component	Mitochondrion	HTP	34800366
GO:0005739	Component	Mitochondrion	IBA
GO:0005739	Component	Mitochondrion	IEA
GO:0005759	Component	Mitochondrial matrix	TAS
GO:0005829	Component	Cytosol	IDA
GO:0005829	Component	Cytosol	TAS
GO:0006412	Process	Translation	IEA
GO:0006418	Process	TRNA aminoacylation for protein translation	IEA
GO:0006418	Process	TRNA aminoacylation for protein translation	IMP	28675565
GO:0006426	Process	Glycyl-tRNA aminoacylation	IEA
GO:0006426	Process	Glycyl-tRNA aminoacylation	IEA
GO:0015966	Process	Diadenosine tetraphosphate biosynthetic process	IDA	19710017
GO:0016740	Function	Transferase activity	IEA
GO:0016787	Function	Hydrolase activity	IEA
GO:0016874	Function	Ligase activity	IEA
GO:0030141	Component	Secretory granule	IEA
GO:0030424	Component	Axon	IDA	17035524
GO:0030424	Component	Axon	IEA
GO:0042802	Function	Identical protein binding	IPI	17545306, 17595294
GO:0042995	Component	Cell projection	IEA
GO:0046983	Function	Protein dimerization activity	IDA	17544401, 17545306
GO:0070062	Component	Extracellular exosome	IEA
GO:0070062	Component	Extracellular exosome	ISS
GO:0070150	Process	Mitochondrial glycyl-tRNA aminoacylation	IBA
GO:0141192	Function	ATP:ATP adenylyltransferase activity	IEA

MIM	HGNC	e!Ensembl
600287	4162	ENSG00000106105

Protein

UniProt ID

P41250

Protein name

Glycine--tRNA ligase (EC 6.1.1.14) (Diadenosine tetraphosphate synthetase) (Ap4A synthetase) (EC 2.7.7.-) (Glycyl-tRNA synthetase) (GlyRS) (Glycyl-tRNA synthetase 1)

Protein function

Catalyzes the ATP-dependent ligation of glycine to the 3'-end of its cognate tRNA, via the formation of an aminoacyl-adenylate intermediate (Gly-AMP) (PubMed:17544401, PubMed:24898252, PubMed:28675565). Also produces diadenosine tetraphosphate (

PDB

2PME , 2PMF , 2Q5H , 2Q5I , 2ZT5 , 2ZT6 , 2ZT7 , 2ZT8 , 2ZXF , 4KQE , 4KR2 , 4KR3 , 4QEI , 5E6M

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF00458	WHEP-TRS	67 → 117	WHEP-TRS domain	Domain
PF00587	tRNA-synt_2b	291 → 592	tRNA synthetase class II core domain (G, H, P, S and T)	Domain
PF03129	HGTP_anticodon	615 → 709	Anticodon binding domain	Domain

Tissue specificity

TISSUE SPECIFICITY: Widely expressed, including in brain and spinal cord. {ECO:0000269|PubMed:12690580}.; TISSUE SPECIFICITY: [Isoform 2]: Expressed in brain, spinal cord, muscle, heart and spleen. {ECO:0000269|PubMed:26327585}.; TISSUE SPECIFICITY: [Isof

Sequence

MPSPRPVLLRGARAALLLLLPPRLLARPSLLLRRSLSAASCPPISLPAAASRSSMDGAGA
EEVLAPLRLAVRQQGDLVRKLKEDKAPQVDVDKAVAELKARKRVLEAKELALQPKDDIVD
RAKMEDTLKRRFFYDQAFAIYGGVSGLYDFGPVGCALKNNIIQTWRQHFIQEEQILEIDC
TMLTPEPVLKTSGHVDKFADFMVKDVKNGECFRADHLLKAHLQKLMSDKKCSVEKKSEME
SVLAQLDNYGQQELADLFVNYNVKSPITGNDLSPPVSFNLMFKTFIGPGGNMPGYLRPET
AQGIFLNFKRLLEFNQGKLPFAAAQIGNSFRNEISPRSGLIRVREFTMAEIEHFVDPSEK
DHPKFQNVADLHLYLYSAKAQVSGQSARKMRLGDAVEQGVINNTVLGYFIGRIYLYLTKV
GISPDKLRFRQHMENEMAHYACDCWDAESKTSYGWIEIVGCADRSCYDLSCHARATKVPL
VAEKPLKEPKTVNVVQFEPSKGAIGKAYKKDAKLVMEYLAICDECYITEMEMLLNEKGEF
TIETEGKTFQLTKDMINVKRFQKTLYVEEVVPNVIEPSFGLGRIMYTVFEHTFHVREGDE
QRTFFSFPAVVAPFKCSVLPLSQNQEFMPFVKELSEALTRHGVSHKVDDSSGSIGRRYAR
TDEIGVAFGVTIDFDTVNKTPHTATLRDRDSMRQIRAEISELPSIVQDLANGNITWADVE
ARYPLFEGQETGKKETIEE

Sequence length

739

Interactions

View interactions

	KEGG		Reactome
	Aminoacyl-tRNA biosynthesis		Cytosolic tRNA aminoacylation Mitochondrial tRNA aminoacylation

Show/Hide Causal Diseases (4)

Disease merge term	Disease name	dbSNP ID	References
Causal Diseases caused by PATHOGENIC or LIKELY PATHOGENIC variants from ClinVar only
Charcot-Marie-Tooth Disease	Charcot-Marie-Tooth disease type 2, Charcot-Marie-Tooth disease type 2D, Charcot-Marie-Tooth Disease	rs1060502838, rs1554337974, rs1301948344, rs137852643, rs1584034430, rs1554338262, rs137852644, rs1060502839, rs1064795123, rs1554338641, rs1554338260, rs137852646, rs1554337369	N/A
Distal Hereditary Motor Neuronopathy	Neuronopathy, distal hereditary motor, type 5A	rs137852644, rs1584034430, rs137852646, rs1584026191, rs1554338260, rs1060502838	N/A
Distal Spinal Muscular Atrophy	distal spinal muscular atrophy	rs1060502838, rs137852646, rs1554338260	N/A
Spinal Muscular Atrophy	Spinal muscular atrophy, infantile, James type	rs1554338262, rs797044855	N/A

Show/Hide Unknown Diseases (2)

Disease merge term	Disease name	Evidence	References	Source
Unknown Includes: (1) ClinVar NON-pathogenic variants (Uncertain, Benign, Conflicting, VUS), (2) GenCC associations, (3) GWAS associations, (4) CBGDA evidence-based associations. NOTE: Diseases with pathogenic evidence are excluded to avoid conflicts.
Motor Neuron Disease	motor neuron disease	N/A	N/A	ClinVar
Peripheral axonal neuropathy	peripheral axonal neuropathy	N/A	N/A	ClinVar

Show/Hide Text Mining Associations (33)

Disease Name	Relationship Type	References
Associations from Text Mining Disease associations identified through Pubtator
Atrophy	Associate	22462675
Charcot Marie Tooth Disease	Associate	17142907, 17545306, 21737751, 24669931, 24898252, 28675565, 31173493, 31501329, 33753480, 34403468
Charcot Marie Tooth disease Type 2D	Associate	12690580, 19412816, 22462675, 28594869, 31173493, 31985473, 34958183
Disease	Associate	28675565
Distal Hereditary Motor Neuropathy Type II	Associate	31628756
Down Syndrome	Associate	22931243
Failure to Thrive	Associate	31985473
Feeding and Eating Disorders	Associate	31985473
Genetic Diseases Inborn	Associate	12690580, 17544401
Growth Disorders	Associate	28675565
Heredodegenerative Disorders Nervous System	Associate	26797133
Hyperekplexia	Associate	35526563
Hyperexplexia hereditary	Associate	7518444
Isolated Noncompaction of the Ventricular Myocardium	Associate	24669931
Liver Cirrhosis	Associate	29666468
Lymphatic Metastasis	Stimulate	36901698
Mitochondrial Diseases	Associate	24669931, 25058219, 28594869
Motor Neuron Disease	Associate	12690580
Multiple System Atrophy	Associate	28675565
Muscle Weakness	Associate	22462675, 31628756
Muscular Atrophy Spinal	Associate	17544401, 24669931, 32181591
Neoplasms	Associate	27348078
Neoplastic Syndromes Hereditary	Associate	31985473
Nerve Degeneration	Associate	17544401
Nervous System Diseases	Associate	31985473
Neuronopathy Distal Hereditary Motor Type I	Associate	19412816
Neuronopathy Distal Hereditary Motor Type V	Associate	12690580, 17663003, 22462675, 28594869, 31985473
Peripheral Nervous System Diseases	Associate	21737751
Prostatic Neoplasms	Associate	36901698
Shoulder Fractures	Associate	31628756
Spastic Paraplegia Hereditary	Associate	19412816, 22462675
Spinal muscular atrophy Jerash type	Associate	31628756
Stiff Person Syndrome	Associate	28174298

GARS1 (glycyl-tRNA synthetase 1)