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.	7407
Gene name Gene Name - the full gene name approved by the HGNC.	Valyl-tRNA synthetase 1
Gene symbol Gene Symbol - the official gene symbol approved by the HGNC.	VARS1
Synonyms (NCBI Gene) Gene synonyms aliases	G7A, NDMSCA, VARS, VARS2
Chromosome Chromosome number	6
Chromosome location Chromosomal Location - indicates the cytogenetic location of the gene or region on the chromosome.	6p21.33
Summary Summary of gene provided in NCBI Entrez Gene.	Aminoacyl-tRNA synthetases catalyze the aminoacylation of tRNA by their cognate amino acid. Because of their central role in linking amino acids with nucleotide triplets contained in tRNAs, aminoacyl-tRNA synthetases are thought to be among the first prot

Show/Hide all(16)

SNP ID	Visualize variation	Clinical significance	Consequence
rs149378938	G>A,C	Likely-pathogenic	Genic downstream transcript variant, coding sequence variant, missense variant
rs150882285	C>A,T	Likely-pathogenic	Coding sequence variant, missense variant, non coding transcript variant
rs376864621	C>T	Pathogenic	Missense variant, non coding transcript variant, coding sequence variant
rs747824231	C>G,T	Pathogenic	Non coding transcript variant, coding sequence variant, missense variant
rs749228986	G>A	Uncertain-significance, pathogenic	Missense variant, 5 prime UTR variant, coding sequence variant, non coding transcript variant
rs757026184	->CTGGGCCACAGCCG	Pathogenic	Genic upstream transcript variant, coding sequence variant, non coding transcript variant, frameshift variant
rs762729609	C>G,T	Pathogenic	5 prime UTR variant, missense variant, coding sequence variant, non coding transcript variant
rs763777257	G>A	Pathogenic	5 prime UTR variant, stop gained, coding sequence variant, non coding transcript variant
rs769369302	C>T	Pathogenic, likely-pathogenic	Genic downstream transcript variant, coding sequence variant, missense variant, downstream transcript variant
rs1060499734	G>A	Likely-pathogenic, pathogenic	Non coding transcript variant, coding sequence variant, missense variant
rs1336685414	C>T	Pathogenic	Missense variant, coding sequence variant, non coding transcript variant
rs1401228799	G>T	Likely-pathogenic	Missense variant, non coding transcript variant, coding sequence variant
rs1562293093	C>T	Pathogenic	Missense variant, genic downstream transcript variant, coding sequence variant, downstream transcript variant
rs1562301511	T>C	Pathogenic	Splice acceptor variant, intron variant
rs1562303235	G>C	Pathogenic	Missense variant, 5 prime UTR variant, coding sequence variant, non coding transcript variant
rs1562303844	T>G	Pathogenic	Missense variant, 5 prime UTR variant, coding sequence variant, non coding transcript variant

Show/Hide all(20)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000166	Function	Nucleotide binding	IEA
GO:0002161	Function	Aminoacyl-tRNA deacylase activity	IEA
GO:0004812	Function	Aminoacyl-tRNA ligase activity	IEA
GO:0004832	Function	Valine-tRNA ligase activity	IBA
GO:0004832	Function	Valine-tRNA ligase activity	IDA	8428657
GO:0004832	Function	Valine-tRNA ligase activity	IEA
GO:0004832	Function	Valine-tRNA ligase activity	TAS
GO:0005515	Function	Protein binding	IPI	24965446, 25416956, 32296183
GO:0005524	Function	ATP binding	IEA
GO:0005783	Component	Endoplasmic reticulum	IDA
GO:0005829	Component	Cytosol	IBA
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	TAS
GO:0006438	Process	Valyl-tRNA aminoacylation	IBA
GO:0006438	Process	Valyl-tRNA aminoacylation	IEA
GO:0016874	Function	Ligase activity	IEA
GO:0106074	Process	Aminoacyl-tRNA metabolism involved in translational fidelity	IEA

MIM	HGNC	e!Ensembl
192150	12651	ENSG00000204394

Protein

UniProt ID

P26640

Protein name

Valine--tRNA ligase (EC 6.1.1.9) (Protein G7a) (Valyl-tRNA synthetase) (ValRS)

Protein function

Catalyzes the attachment of valine to tRNA(Val).

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF00043	GST_C	97 → 198	Glutathione S-transferase, C-terminal domain	Domain
PF00133	tRNA-synt_1	308 → 939	tRNA synthetases class I (I, L, M and V)	Family
PF08264	Anticodon_1	984 → 1139	Anticodon-binding domain of tRNA ligase	Domain

Sequence

MSTLYVSPHPDAFPSLRALIAARYGEAGEGPGWGGAHPRICLQPPPTSRTPFPPPRLPAL
EQGPGGLWVWGATAVAQLLWPAGLGGPGGSRAAVLVQQWVSYADTELIPAACGATLPALG
LRSSAQDPQAVLGALGRALSPLEEWLRLHTYLAGEAPTLADLAAVTALLLPFRYVLDPPA
RRIWNNVTRWFVTCVRQPEFRAVLGEVVLYSGARPLSHQPGPEAPALPKTAAQLKKEAKK
REKLEKFQQKQKIQQQQPPPGEKKPKPEKREKRDPGVITYDLPTPPGEKKDVSGPMPDSY
SPRYVEAAWYPWWEQQGFFKPEYGRPNVSAANPRGVFMMCIPPPNVTGSLHLGHALTNAI
QDSLTRWHRMRGETTLWNPGCDHAGIATQVVVEKKLWREQGLSRHQLGREAFLQEVWKWK
EEKGDRIYHQLKKLGSSLDWDRACFTMDPKLSAAVTEAFVRLHEEGIIYRSTRLVNWSCT
LNSAISDIEVDKKELTGRTLLSVPGYKEKVEFGVLVSFAYKVQGSDSDEEVVVATTRIET
MLGDVAVAVHPKDTRYQHLKGKNVIHPFLSRSLPIVFDEFVDMDFGTGAVKITPAHDQND
YEVGQRHGLEAISIMDSRGALINVPPPFLGLPRFEARKAVLVALKERGLFRGIEDNPMVV
PLCNRSKDVVEPLLRPQWYVRCGEMAQAASAAVTRGDLRILPEAHQRTWHAWMDNIREWC
ISRQLWWGHRIPAYFVTVSDPAVPPGEDPDGRYWVSGRNEAEAREKAAKEFGVSPDKISL
QQDEDVLDTWFSSGLFPLSILGWPNQSEDLSVFYPGTLLETGHDILFFWVARMVMLGLKL
TGRLPFREVYLHAIVRDAHGRKMSKSLGNVIDPLDVIYGISLQGLHNQLLNSNLDPSEVE
KAKEGQKADFPAGIPECGTDALRFGLCAYMSQGRDINLDVNRILGYRHFCNKLWNATKFA
LRGLGKGFVPSPTSQPGGHESLVDRWIRSRLTEAVRLSNQGFQAYDFPAVTTAQYSFWLY
ELCDVYLECLKPVLNGVDQVAAECARQTLYTCLDVGLRLLSPFMPFVTEELFQRLPRRMP
QAPPSLCVTPYPEPSECSWKDPEAEAALELALSITRAVRSLRADYNLTRIRPDCFLEVAD
EATGALASAVSGYVQALASAGVVAVLALGAPAPQGCAVALASDRCSIHLQLQGLVDPARE
LGKLQAKRVEAQRQAQRLRERRAASGYPVKVPLEVQEADEAKLQQTEAELRKVDEAIALF
QKML

Sequence length

1264

Interactions

View interactions

	KEGG		Reactome
	Aminoacyl-tRNA biosynthesis		Cytosolic tRNA aminoacylation

Show/Hide Causal Diseases (1)

Disease merge term	Disease name	dbSNP ID	References
Causal Diseases caused by PATHOGENIC or LIKELY PATHOGENIC variants from ClinVar only
Neurodevelopmental Disorder With Microcephaly, Seizures, And Cortical Atrophy	neurodevelopmental disorder with microcephaly, seizures, and cortical atrophy	rs1562303235, rs757026184, rs1562301511, rs1562293093, rs776596987, rs769369302, rs747824231, rs763777257, rs149378938, rs1336685414, rs376864621	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.
Combined Oxidative Phosphorylation Deficiency	combined oxidative phosphorylation defect type 20	N/A	N/A	GenCC
Psoriasis	Psoriasis	N/A	N/A	GWAS

Show/Hide Text Mining Associations (20)

Disease Name	Relationship Type	References
Associations from Text Mining Disease associations identified through Pubtator
Atrophy	Associate	29691655
Autosomal Recessive Primary Microcephaly	Associate	30755602
Brain Diseases	Associate	30755602
Breast Neoplasms	Associate	39940786
Diabetes Mellitus Type 2	Associate	31932636
Epilepsia Partialis Continua	Associate	29314548
Intellectual Disability	Associate	30755602
Melanoma	Associate	36303162
Microcephaly	Associate	29691655
Mitochondrial Diseases	Associate	29314548
Mitochondrial encephalopathy	Associate	31064326
Multiple Myeloma	Associate	37587064
Neoplasms	Associate	30381327, 36303162
Neurodegenerative Diseases	Associate	30755602
Ovarian Neoplasms	Associate	34793589
Pena Shokeir syndrome type 1	Associate	34636181
Psychomotor Disorders	Associate	29314548
Sarcoma Kaposi	Associate	25008864
Seizures	Associate	29691655
Tremor	Associate	34636181

VARS1 (valyl-tRNA synthetase 1)