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

Gene Gene information from NCBI Gene database. Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID	57176
Gene name	Valyl-tRNA synthetase 2, mitochondrial
Gene symbol	VARS2
Synonyms (NCBI Gene)	COXPD20VALRSVARS2LVARSL
Chromosome	6
Chromosome location	6p21.33
Summary	This gene encodes a mitochondrial aminoacyl-tRNA synthetase, which catalyzes the attachment of valine to tRNA(Val) for mitochondrial translation. Mutations in this gene cause combined oxidative phosphorylation deficiency-20, and are also associated with e

Show/Hide all (9)

SNP ID	Visualize variation	Clinical significance	Consequence
rs139515727	C>T	Likely-pathogenic	Missense variant, coding sequence variant
rs202201763	G>A	Uncertain-significance, conflicting-interpretations-of-pathogenicity	Coding sequence variant, missense variant
rs587777583	G>A	Pathogenic	Missense variant, coding sequence variant
rs587777584	C>A	Pathogenic	Missense variant, coding sequence variant
rs587777585	C>G,T	Pathogenic	Missense variant, coding sequence variant
rs775439829	G>A,C	Likely-pathogenic	Missense variant, coding sequence variant
rs777028011	CT>-	Likely-pathogenic	Frameshift variant, coding sequence variant
rs1554268077	GGG>-	Likely-pathogenic	Coding sequence variant, inframe deletion
rs1582173192	->GATG	Likely-pathogenic	Coding sequence variant, frameshift variant

Show/Hide all (9)

miRTarBase ID	miRNA	Experiments
MIRT1482783	hsa-miR-1827	CLIP-seq
MIRT1482784	hsa-miR-3612	CLIP-seq
MIRT1482785	hsa-miR-650	CLIP-seq
MIRT1482786	hsa-miR-940	CLIP-seq
MIRT2659277	hsa-miR-2355-3p	CLIP-seq
MIRT2659278	hsa-miR-3909	CLIP-seq
MIRT2659279	hsa-miR-4646-3p	CLIP-seq
MIRT2659280	hsa-miR-4762-5p	CLIP-seq
MIRT2659281	hsa-miR-676	CLIP-seq

Show/Hide all (17)

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	IEA
GO:0004832	Function	Valine-tRNA ligase activity	IMP	24827421
GO:0005515	Function	Protein binding	IPI	25416956, 32296183
GO:0005524	Function	ATP binding	IEA
GO:0005739	Component	Mitochondrion	HTP	34800366
GO:0005739	Component	Mitochondrion	IEA
GO:0005829	Component	Cytosol	IBA
GO:0006412	Process	Translation	IEA
GO:0006418	Process	TRNA aminoacylation for protein translation	IEA
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
612802	21642	ENSG00000137411

Q5ST30

Protein name

Valine--tRNA ligase, mitochondrial (EC 6.1.1.9) (Valyl-tRNA synthetase) (ValRS) (Valyl-tRNA synthetase-like)

Protein function

Catalyzes the attachment of valine to tRNA(Val) in a two-step reaction: valine is first activated by ATP to form Val-AMP and then transferred to the acceptor end of tRNA(Val).

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF00133	tRNA-synt_1	112 → 735	tRNA synthetases class I (I, L, M and V)	Family
PF08264	Anticodon_1	779 → 932	Anticodon-binding domain of tRNA ligase	Domain

Sequence

MPHLPLASFRPPFWGLRHSRGLPRFHSVSTQSEPHGSPISRRNREAKQKRLREKQATLEA
EIAGESKSPAESIKAWRPKELVLYEIPTKPGEKKDVSGPLPPAYSPRYVEAAWYPWWVRE
GFFKPEYQARLPQATGETFSMCIPPPNVTGSLHIGHALTVAIQDALVRWHRMRGDQVLWV
PGSDHAGIATQAVVEKQLWKERGVRRHELSREAFLREVWQWKEAKGGEICEQLRALGASL
DWDRECFTMDVGSSVAVTEAFVRLYKAGLLYRNHQLVNWSCALRSAISDIEVENRPLPGH
TQLRLPGCPTPVSFGLLFSVAFPVDGEPDAEVVVGTTRPETLPGDVAVAVHPDDSRYTHL
HGRQLRHPLMGQPLPLITDYAVQPHVGTGAVKVTPAHSPADAEMGARHGLSPLNVIAEDG
TMTSLCGDWLQGLHRFVAREKIMSVLSEWGLFRGLQNHPMVLPICSRSGDVIEYLLKNQW
FVRCQEMGARAAKAVESGALELSPSFHQKNWQHWFSHIGDWCVSRQLWWGHQIPAYLVVE
DHAQGEEDCWVVGRSEAEAREVAAELTGRPGAELTLERDPDVLDTWFSSALFPFSALGWP
QETPDLARFYPLSLLETGSDLLLFWVGRMVMLGTQLTGQLPFSKVLLHPMVRDRQGRKMS
KSLGNVLDPRDIISGVEMQVLQEKLRSGNLDPAELAIVAAAQKKDFPHGIPECGTDALRF
TLCSHGVQAGDLHLSVSEVQSCRHFCNKIWNALRFILNALGEKFVPQPAEELSPSSPMDA
WILSRLALAAQECERGFLTRELSLVTHALHHFWLHNLCDVYLEAVKPVLWHSPRPLGPPQ
VLFSCADLGLRLLAPLMPFLAEELWQRLPPRPGCPPAPSISVAPYPSACSLEHWRQPELE
RRFSRVQEVVQVLRALRATYQLTKARPRVLLQSSEPGDQGLFEAFLEPLGTLGYCGAVGL
LPPGAAAPSGWAQAPLSDTAQVYMELQGLVDPQIQLPLLAARRYKLQKQLDSLTARTPSE
GEAGTQRQQKLSSLQLELSKLDKAASHLRQLMDEPPAPGSPEL

Sequence length

1063

Interactions

View interactions

	KEGG
	Aminoacyl-tRNA biosynthesis

113

Show/Hide Causal Diseases (2)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Adrenocortical carcinoma, hereditary	Likely pathogenic; Pathogenic	rs200075594	RCV005908962
Combined oxidative phosphorylation defect type 20	Likely pathogenic; Pathogenic	rs1794789052, rs769768815, rs2150548621, rs2150570235, rs587777583, rs587777584, rs587777585, rs2538661360, rs753139152, rs1554268192, rs1434914864, rs2538630404, rs775439829, rs1554268077, rs777028011 View all (5 more)	RCV001330431 RCV001334847 RCV005395087 RCV001808112 RCV000129933 RCV000129935 RCV000129937 RCV002288233 RCV002472145 RCV003324208 RCV003332014 RCV004595400 RCV000578459 RCV000578269 RCV000987662 RCV001201407 RCV001201409 RCV001201410 RCV001201411 RCV001293011

Show/Hide Unknown Diseases (14)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
Acute myeloid leukemia	Uncertain significance	rs144112557, rs1478306971	RCV005924188 RCV005928356
Cervical cancer	Uncertain significance	rs771305166	RCV005924292
Familial cancer of breast	Likely benign; Uncertain significance	rs184436050, rs745703050	RCV005930346 RCV005935030
Gastric cancer	Benign; Likely benign; Uncertain significance	rs540706100, rs756098228, rs184436050	RCV005867123 RCV005924193 RCV005930349
Germ cell tumor of testis	Benign	rs2074506	RCV005896358
Hepatocellular carcinoma	Benign	rs2074506	RCV005896357
Hepatoencephalopathy due to combined oxidative phosphorylation defect type 1	Uncertain significance	rs1562465419	RCV000714819
Malignant lymphoma, large B-cell, diffuse	Likely benign	rs189316271, rs184436050	RCV005920668 RCV005930348
Malignant tumor of esophagus	Benign; Likely benign	rs540706100, rs184436050	RCV005867121 RCV005930347
Melanoma	Likely benign	rs184436050	RCV005930351
Nonpapillary renal cell carcinoma	Benign; Likely benign	rs540706100	RCV005867122
See cases	Uncertain significance; Conflicting classifications of pathogenicity	rs148448090, rs202201763	RCV002252364 RCV002252181
Thyroid cancer, nonmedullary, 1	Likely benign; Benign	rs184436050, rs753726	RCV005930350 RCV005896359
VARS2-related disorder	Uncertain significance; Benign; Likely benign; Conflicting classifications of pathogenicity	rs570231965, rs759325866, rs546690497, rs201758263, rs148172787, rs192370302, rs200841762, rs867938374, rs756787425, rs200908750, rs142520878, rs147636694, rs141974166, rs528281614, rs141408930 View all (4 more)	RCV004548181 RCV004550277 RCV004551993 RCV004553838 RCV004553756 RCV004553757 RCV004548443 RCV004548679 RCV004552802 RCV004554405 RCV004739717 RCV004739725 RCV004551480 RCV004551459 RCV004551599 RCV004547726 RCV004547737 RCV004547763 RCV003336164

Show/Hide Text Mining Associations (42)

Disease Name	Relationship Type	References
Associations from Text MiningDisease associations identified through Pubtator
Acidosis	Associate	30458719
Acidosis Lactic	Associate	30458719
Agenesis of Corpus Callosum	Associate	31064326
Alcohol Related Disorders	Associate	31623496
Arrhythmias Cardiac	Associate	31623496
Arthritis Rheumatoid	Associate	19116923
Ataxia	Associate	29137650
Brain Diseases	Associate	31623496
Cardiomyopathies	Associate	29314548, 30458719
Cardiomyopathy Hypertrophic	Associate	30458719
Cardiovascular Abnormalities	Associate	30458719
Cerebellar Diseases	Associate	31064326
Death	Associate	31064326
Developmental Disabilities	Associate	31064326
Drug Resistant Epilepsy	Associate	31064326
Dwarfism Pituitary	Associate	29137650
Epilepsia Partialis Continua	Associate	29314548
Epilepsy	Associate	24827421, 29137650
Fatigue Syndrome Chronic	Associate	34403736
Feeding and Eating Disorders	Associate	29314548
Genetic Diseases Inborn	Associate	24827421
Growth Disorders	Associate	29137650
Hypogonadism	Associate	29137650
Immunologic Deficiency Syndromes	Associate	30458719
Immunologic Deficiency Syndromes	Inhibit	30458719
Intellectual Disability	Associate	29137650
Kearns Sayre Syndrome	Associate	30925032
Lung Neoplasms	Associate	36634566
Microcephaly	Associate	24827421
Mitochondrial Diseases	Associate	24827421, 25058219, 29314548, 30458719
Mitochondrial Encephalomyopathies	Associate	24827421, 29314548
Mitochondrial encephalopathy	Associate	24827421, 31064326
Muscle Hypertonia	Associate	30458719
Muscle Hypotonia	Associate	29314548, 31064326
Muscle Spasticity	Associate	31064326
Obesity	Associate	31487037
Pediatric acute onset neuropsychiatric syndrome	Associate	31487037
Persistent Fetal Circulation Syndrome	Associate	30458719
Pneumonia	Associate	31487037
Psychomotor Disorders	Associate	29314548, 31064326
Reflex Abnormal	Associate	30458719
Seizures	Associate	29314548

VARS2 (valyl-tRNA synthetase 2, mitochondrial)