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TARS2

gene
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Also known as FLJ12528

Summary

TARS2 (threonyl-tRNA synthetase 2, mitochondrial, HGNC:30740) is a protein-coding gene on chromosome 1q21.2, encoding Threonine–tRNA ligase, mitochondrial (Q9BW92). Catalyzes the attachment of threonine to tRNA(Thr) in a two-step reaction: threonine is first activated by ATP to form Thr-AMP and then transferred to the acceptor end of tRNA(Thr). It is a selective cancer dependency (DepMap: 73.8% of cell lines).

This gene encodes a member of the class-II aminoacyl-tRNA synthetase family. The encoded protein is a mitochondrial aminoacyl-tRNA synthetase. Alternative splicing results in multiple transcript variants. A related pseudogene has been identified on chromosome 4.

Source: NCBI Gene 80222 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): mitochondrial disease (Definitive, ClinGen) — +2 more curated relationships
  • GWAS associations: 17
  • Clinical variants (ClinVar): 352 total — 2 pathogenic, 16 likely-pathogenic (top 9% of genes corpus-wide)
  • GTEx eGene: eQTL in 39 tissues, sQTL in 15 (q < 0.05)
  • Phenotypes (HPO): 16
  • Cancer dependency (DepMap): dependent in 73.8% of screened cell lines
  • Constraint (gnomAD): pLI 0.00 (LoF-tolerant), LOEUF 0.76 (unconstrained)
  • MANE Select transcript: NM_025150

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:30740
Approved symbolTARS2
Namethreonyl-tRNA synthetase 2, mitochondrial
Location1q21.2
Locus typegene with protein product
StatusApproved
AliasesFLJ12528
Ensembl geneENSG00000143374
Ensembl biotypeprotein_coding
OMIM612805
Entrez80222

Gene structure

Transcript identifiers

Ensembl transcripts: 57 — 28 protein_coding, 21 nonsense_mediated_decay, 5 retained_intron, 3 protein_coding_CDS_not_defined

MANE Select: ENST00000369064

Transcript support level (Ensembl TSL; 1 = fully mRNA-supported): TSL 1: 2, TSL 2: 4, TSL 3: 2, TSL 5: 5

ENST00000369064, ENST00000369051, ENST00000369053, ENST00000369054, ENST00000460794, ENST00000462578, ENST00000463555, ENST00000466989, ENST00000467982, ENST00000479372, ENST00000480070, ENST00000483046, ENST00000606933, ENST00000895420, ENST00000895421, ENST00000895422, ENST00000895423, ENST00000895424, ENST00000895425, ENST00000895426, ENST00000895427, ENST00000895428, ENST00000923165, ENST00000923166, ENST00000923167, ENST00000923168, ENST00000923169, ENST00000923170, ENST00000923171, ENST00000923172, ENST00000923173, ENST00000948114, ENST00000984830, ENST00000984831, ENST00000984832, ENST00000984833, ENST00000984834, ENST00000984835, ENST00001020868, ENST00001020870, ENST00001020872, ENST00001020874, ENST00001020875, ENST00001020876, ENST00001075501, ENST00001075502, ENST00001075503, ENST00001075504, ENST00001075505, ENST00001075506, ENST00001075507, ENST00001103294, ENST00001103295, ENST00001103296, ENST00001126752, ENST00001126753, ENST00001142906

RefSeq mRNA: 3 — MANE Select: NM_025150 NM_001271895, NM_001271896, NM_025150

CCDS: CCDS60251, CCDS60252, CCDS952

Canonical transcript exons

ENST00000369064 — 18 exons

ExonStartEnd
ENSE00000959658150490601150490725
ENSE00001448725150506916150507602
ENSE00002228064150487419150487516
ENSE00003458298150496482150496628
ENSE00003482095150491394150491511
ENSE00003604445150496810150496908
ENSE00003667634150491598150491662
ENSE00003694893150497530150497747
ENSE00003695801150492411150492489
ENSE00003696240150505591150505705
ENSE00003696402150504906150504978
ENSE00003696948150499216150499293
ENSE00003698259150498502150498664
ENSE00003700057150504335150504435
ENSE00003700321150488964150489087
ENSE00003700676150498897150499034
ENSE00003702024150504632150504733
ENSE00003723358150487858150488054

Expression profiles

Bgee: expression breadth ubiquitous, 254 present calls, max score 91.25.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 24.6934 / max 463.3193, expressed in 1811 samples.

Highest expression (Bgee): gastrocnemius, apex of heart, muscle of leg, hindlimb stylopod muscle, cerebellar vermis.

Genetic regulation across tissues (GTEx eQTL / sQTL)

TARS2 is an eGene in GTEx v10 — its expression is genetically regulated (eQTL) in 39 tissues and its splicing (sQTL) in 15 (q < 0.05). Strongest associations first; slope = normalized effect of the lead variant’s alternative allele.

showing 20 of 54 significant tissue × QTL associations:

TissueQTLq-valueSlopeLead variant
Muscle Skeletaleqtl1.8e-23-0.191:150348590:T:G
Cells Cultured fibroblastseqtl2.0e-20+0.661:150496780:G:T
Artery Tibialeqtl1.9e-15+0.791:150359534:C:T
Nerve Tibialeqtl3.9e-15+0.861:150298822:G:A
Skin Sun Exposed Lower legeqtl2.0e-13-0.201:150521449:C:G
Adipose Subcutaneouseqtl3.1e-13+0.241:150322682:T:G
Esophagus Mucosaeqtl3.8e-13+0.921:150494737:C:CA
Thyroideqtl2.7e-11+0.681:150285405:G:A
Esophagus Gastroesophageal Junctioneqtl5.0e-11+0.921:150494737:C:CA
Brain Cerebellar Hemisphereeqtl9.3e-10+1.291:150274698:C:T
Skin Not Sun Exposed Suprapubiceqtl1.3e-09-0.201:150521449:C:G
Adipose Visceral Omentumeqtl1.0e-08-0.161:150521449:C:G
Breast Mammary Tissueeqtl1.2e-08-0.221:150521449:C:G
Artery Aortaeqtl1.2e-08+0.811:150293419:A:C
Esophagus Musculariseqtl4.2e-08+0.731:150517894:C:T
Brain Cerebellar Hemispheresqtl8.6e-08+1.481:150416469:A:T
Brain Frontal Cortex BA9eqtl1.3e-06+0.321:150276941:G:GA
Heart Left Ventricleeqtl1.6e-06-0.131:150432822:T:C
Brain Cerebellumeqtl1.9e-06+1.301:150274698:C:T
Heart Atrial Appendageeqtl3.0e-06+0.131:150283177:T:C

FANTOM5 promoters

1 alternative TSS:

Promoter IDTPM avgSamples expressed
510624.69341811

Top tissues by expression

showing 100 of 281 tissues by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
gastrocnemiusUBERON:000138891.25gold quality
apex of heartUBERON:000209891.18gold quality
muscle of legUBERON:000138391.07gold quality
hindlimb stylopod muscleUBERON:000425290.50gold quality
cerebellar vermisUBERON:000472090.04gold quality
triceps brachiiUBERON:000150989.60silver quality
right adrenal glandUBERON:000123389.57gold quality
muscle organUBERON:000163089.45gold quality
heart left ventricleUBERON:000208489.10gold quality
right hemisphere of cerebellumUBERON:001489089.04gold quality
cerebellar cortexUBERON:000212988.98gold quality
cerebellar hemisphereUBERON:000224588.98gold quality
cardiac ventricleUBERON:000208288.82gold quality
buccal mucosa cellCL:000233688.80silver quality
right lobe of liverUBERON:000111488.71gold quality
right frontal lobeUBERON:000281088.58gold quality
right adrenal gland cortexUBERON:003582788.52gold quality
left adrenal glandUBERON:000123488.50gold quality
left adrenal gland cortexUBERON:003582588.17gold quality
lower esophagus mucosaUBERON:003583488.13gold quality
prefrontal cortexUBERON:000045188.01gold quality
granulocyteCL:000009487.95gold quality
adrenal cortexUBERON:000123587.91gold quality
cerebellumUBERON:000203787.91gold quality
adrenal glandUBERON:000236987.70gold quality
right atrium auricular regionUBERON:000663187.62gold quality
skin of legUBERON:000151187.41gold quality
right ovaryUBERON:000211887.29gold quality
Brodmann (1909) area 9UBERON:001354087.27gold quality
left ovaryUBERON:000211987.15gold quality
tibial nerveUBERON:000132387.10gold quality
anterior cingulate cortexUBERON:000983587.02gold quality
right uterine tubeUBERON:000130287.00gold quality
cingulate cortexUBERON:000302786.98gold quality
heartUBERON:000094886.97gold quality
right lobe of thyroid glandUBERON:000111986.89gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099186.87gold quality
cardiac atriumUBERON:000208186.56gold quality
gluteal muscleUBERON:000200086.41silver quality
nucleus accumbensUBERON:000188286.40gold quality
ectocervixUBERON:001224986.34gold quality
esophagus mucosaUBERON:000246986.29gold quality
spleenUBERON:000210686.21gold quality
C1 segment of cervical spinal cordUBERON:000646986.12gold quality
skin of abdomenUBERON:000141686.05gold quality
body of stomachUBERON:000116186.01gold quality
skeletal muscle tissueUBERON:000113486.00gold quality
frontal cortexUBERON:000187085.90gold quality
adenohypophysisUBERON:000219685.88gold quality
neocortexUBERON:000195085.78gold quality
body of uterusUBERON:000985385.55gold quality
dorsolateral prefrontal cortexUBERON:000983485.53gold quality
mucosa of transverse colonUBERON:000499185.45gold quality
pituitary glandUBERON:000000785.42gold quality
esophagusUBERON:000104385.38gold quality
right testisUBERON:000453485.35gold quality
lymph nodeUBERON:000002985.30gold quality
spinal cordUBERON:000224085.21gold quality
caudate nucleusUBERON:000187385.18gold quality
endocervixUBERON:000045885.07gold quality
stomachUBERON:000094585.07gold quality
fundus of stomachUBERON:000116085.01gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047384.94gold quality
left lobe of thyroid glandUBERON:000112084.94gold quality
amygdalaUBERON:000187684.86gold quality
liverUBERON:000210784.81gold quality
left testisUBERON:000453384.81gold quality
small intestine Peyer’s patchUBERON:000345484.80gold quality
islet of LangerhansUBERON:000000684.75gold quality
body of pancreasUBERON:000115084.74gold quality
body of tongueUBERON:001187684.72silver quality
putamenUBERON:000187484.70gold quality
colonic epitheliumUBERON:000039784.67gold quality
rectumUBERON:000105284.67gold quality
hypothalamusUBERON:000189884.64gold quality
bone marrow cellCL:000209284.63gold quality
adrenal tissueUBERON:001830384.62gold quality
left uterine tubeUBERON:000130384.60gold quality
zone of skinUBERON:000001484.55gold quality
thyroid glandUBERON:000204684.55gold quality
lower esophagusUBERON:001347384.44gold quality
lower esophagus muscularis layerUBERON:003583384.43gold quality
vastus lateralisUBERON:000137984.42silver quality
minor salivary glandUBERON:000183084.41gold quality
esophagogastric junction muscularis propriaUBERON:003584184.41gold quality
muscle tissueUBERON:000238584.39gold quality
quadriceps femorisUBERON:000137784.38silver quality
brainUBERON:000095584.37gold quality
transverse colonUBERON:000115784.35gold quality
ovaryUBERON:000099284.26gold quality
forebrainUBERON:000189084.23gold quality
telencephalonUBERON:000189384.16gold quality
cerebral cortexUBERON:000095684.08gold quality
right coronary arteryUBERON:000162584.08gold quality
subcutaneous adipose tissueUBERON:000219084.07gold quality
stromal cell of endometriumCL:000225584.03gold quality
pancreasUBERON:000126483.99gold quality
mucosa of stomachUBERON:000119983.97gold quality
muscle layer of sigmoid colonUBERON:003580583.94gold quality
small intestineUBERON:000210883.83gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-ANND-3yes4.68

HPA expression

RNA tissue specificity: Low tissue specificity

showing 60 of 80 HPA tissues / cells by nTPM:

Tissue / cellAxisnTPMProtein (IHC)
Skeletal muscletissue29.9medium
Tonguetissue29.0
Putamentissue24.5
Cerebral cortextissue24.4medium
Somatosensory cortextissue24.4
Livertissue23.7medium
Midbraintissue23.4
Cerebellumtissue23.2medium
Superior colliculitissue22.6
Basal gangliatissue22.4medium
Septumtissue22.3
Occipital cortextissue22.3
Hippocampal formationtissue22.0
Hypothalamustissue21.8
Olfactory bulbtissue21.7
Prefrontal cortextissue21.6
Thalamustissue21.6
Ventral forebraintissue21.6
Motor cortextissue21.1
Medulla oblongatatissue21.1
Retrosplenial cortextissue21.0
Retrosplenial and cingulate cortextissue20.9
Periaqueductal graytissue20.9
Temporal cortextissue20.9
Substantia nigratissue20.7
Insular cortextissue20.7
Frontal cortextissue20.6
Amygdalatissue20.5
Entorhinal cortextissue20.5
Caudate putamentissue20.5
Corpus callosumtissue20.2
Ponstissue20.0
Spinal cordtissue19.9
Heart muscletissue19.0medium
Parathyroid glandtissue16.6medium
Locus coeruleustissue16.6
Postcentral gyrustissue16.1
Choroid plexustissue15.4
Nucleus accumbenstissue14.8
Tonsiltissue14.4medium
Lymph nodetissue13.7medium
Retinatissue13.5
Kidneytissue13.3high
Hippocampustissue13.2medium
Epididymistissue12.3medium
Spleentissue11.8medium
Thymustissue11.8
Adrenal glandtissue11.4medium
Stomach 1tissue11.3medium
Fallopian tubetissue11.0medium
Skin 1tissue10.8medium
Esophagustissue10.6medium
Rectumtissue10.6high
Thyroid glandtissue10.5high
Ovarytissue10.3medium
Appendixtissue10.0medium
Colontissue9.7medium
Breasttissue9.6medium
Smooth muscletissue9.3low
Bone marrowtissue9.3medium

Brain sub-regions (HPA Brain Atlas): detected in 192; highest nTPM — Ventral hippocampus (22.0), Dorsal hippocampus (21.0), Subiculum (20.8), White matter (20.2), Dorsal spinal cord (19.9).

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): ATF4, QRICH1

miRNA regulators (miRDB)

Targeting TARS2 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific).

19 miRNAs:

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-4510100.0066.602050
HSA-MIR-6127100.0066.762188
HSA-MIR-6129100.0066.462080
HSA-MIR-6130100.0066.692012
HSA-MIR-6133100.0066.482064
HSA-MIR-9983-3P99.9471.483631
HSA-MIR-145-5P99.9271.131836
HSA-MIR-5195-3P99.9270.921877
HSA-MIR-129-5P99.8870.263273
HSA-MIR-130399.6569.771662
HSA-MIR-3136-3P99.5766.59781
HSA-MIR-7155-3P99.5766.48794
HSA-MIR-4667-3P99.2665.451608
HSA-MIR-427999.1966.702437
HSA-MIR-7151-3P99.0469.722370
HSA-MIR-314998.7767.131639
HSA-MIR-619-5P98.5764.971988
HSA-MIR-10395-3P98.1066.701726
HSA-MIR-3152-5P96.9866.88819

Functional genomics

gnomAD constraint: pLI 1.97e-12, LOEUF 0.76, missense Z 2.91 — population loss-of-function intolerance (pLI ≥ 0.9 = LoF-intolerant; lower LOEUF = more constrained). gnomAD

Regional missense constraint (gnomAD)

ENST00000369064 splits into 3 regions with different missense tolerance; 0 are missense-constrained. Missense variants in a constrained region (low observed/expected) are more likely to be pathogenic. gnomAD

Region (GRCh38)Missense obs / expo/eConstrained
1:150,487,451–150,491,448208 / 228.50.91no
1:150,491,449–150,492,43630 / 64.50.47no
1:150,492,437–150,507,061466 / 609.50.76no
DepMap (CRISPR cell-line fitness): dependent in 73.8% of screened cell lines.

Most-dependent cell lines (DepMap gene-effect, lower = stronger; ≤ −0.5 shown): KYSE-180 (-1.712), COR-L311 (-1.586), ACC-MESO-1 (-1.515), NCI-H2004 RT (-1.512), EOL-1 (-1.51), HMC-1-8 (-1.487), EWS502 (-1.456), F-36P (-1.447), T-47D (-1.431), COR-L23 (-1.418), TE-11 (-1.395), EW8 (-1.388), SF-295 (-1.371), GCIY (-1.363), SNU-1196 (-1.36).

Literature-anchored findings (GeneRIF, showing 5)

  • TARS2 mutations caused fatal mitochondrial encephalomyopathy in two siblings. (PMID:24827421)
  • Identification of a TARS2 splicing variant in several human cell lines, which encodes a hmtThrRS derivative lacking a peptide covering a portion of both the editing and the aminoacylation domains. (PMID:26811336)
  • Novel compound heterozygous TARS2 variants in a Chinese family with mitochondrial encephalomyopathy: a case report. (PMID:33153448)
  • Mitochondrial Threonyl-tRNA Synthetase TARS2 Is Required for Threonine-Sensitive mTORC1 Activation. (PMID:33340489)
  • Clinical, neuroradiological, and molecular characterization of mitochondrial threonyl-tRNA-synthetase (TARS2)-related disorder. (PMID:37454282)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
mus_musculusTars2ENSMUSG00000028107
rattus_norvegicusTars2ENSRNOG00000057194
drosophila_melanogasterThrRSFBGN0027081
caenorhabditis_elegansWBGENE00004189
caenorhabditis_elegansWBGENE00006617

Paralogs (4): TARS1 (ENSG00000113407), MRPL39 (ENSG00000154719), PARS2 (ENSG00000162396), TARS3 (ENSG00000185418)

Mouse-model phenotypes

Observed phenotypes of the mouse ortholog (MGI:1919057) from MGI (Alliance of Genome Resources) — knockout/mutant phenotypes, ranked by annotation count. 3 distinct phenotype terms.

Mouse phenotype (MP)Records
preweaning lethality, complete penetrance1
embryonic lethality prior to organogenesis1
embryonic lethality prior to tooth bud stage1

Additional cross-species homologs

Sequence homologs in species beyond Ensembl Compara’s model organisms, by Diamond local protein alignment (% sequence identity; best hit per species). Lower-identity rows are more distant homologs. The matched accessions’ gene symbols aren’t in biobtree yet, so each row shows the UniProt accession.

OrganismUniProtIdentityMethod
Bos taurusQ3ZBV894.5%Diamond
Xenopus tropicalisQ0V9S081.5%Diamond
Saccharomyces cerevisiae S288CP0480162.9%Diamond
Schizosaccharomyces pombe 972h-P8714462.2%Diamond
Dictyostelium discoideumQ54J6660.0%Diamond
Arabidopsis thalianaO0463057.1%Diamond
Enterocytozoon bieneusi H348B7XIA154.0%Diamond
Encephalitozoon cuniculi GB-M1Q8SRH254.0%Diamond
Aeropyrum pernix K1Q9YFY348.9%Diamond

Genomic neighbors (locus context)

Genes flanking this one on the chromosome (NCBI/Entrez gene neighborhood). Positional context only — some neighbors share regulatory elements (bidirectional promoters, antisense/overlapping transcripts), but chromosomal adjacency is not itself a functional relationship (see Interactions for that).

SymbolTypeEntrez
ADAMTSL4-AS2ncRNA100289061
MIR4257ncRNA100422997
MIR6878ncRNA102465529
ECM1protein-coding1893
ADAMTSL4protein-coding54507
FALECncRNA100874054
RPRD2protein-coding23248
PRPF3protein-coding9129
MRPS21protein-coding54460

Protein

Protein identifiers

Threonine–tRNA ligase, mitochondrial — Q9BW92 (reviewed: Q9BW92)

Alternative names: Threonyl-tRNA synthetase, Threonyl-tRNA synthetase-like 1

All UniProt accessions (5): B4DQF3, Q9BW92, Q5T5E9, U3KQ50, U3KQG0

UniProt curated annotations — full annotation on UniProt →

Function. Catalyzes the attachment of threonine to tRNA(Thr) in a two-step reaction: threonine is first activated by ATP to form Thr-AMP and then transferred to the acceptor end of tRNA(Thr). Also edits incorrectly charged tRNA(Thr) via its editing domain.

Subunit / interactions. Homodimer.

Subcellular location. Mitochondrion matrix.

Disease relevance. Combined oxidative phosphorylation deficiency 21 (COXPD21) [MIM:615918] A mitochondrial disorder characterized by a lethal encephalomyopathy. Shortly after birth, affected individuals manifest axial hypotonia, limb hypertonia, psychomotor delay, and increased serum lactate. Additional features include subsarcolemmal lipofuscin-positive deposits in muscle, cerebral spongiosis, and hepatic steatosis. The disease is caused by variants affecting the gene represented in this entry.

Similarity. Belongs to the class-II aminoacyl-tRNA synthetase family.

Isoforms (2)

UniProt IDNamesCanonical?
Q9BW92-11yes
Q9BW92-22

RefSeq proteins (3): NP_001258824, NP_001258825, NP_079426* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR002314aa-tRNA-synt_IIbDomain
IPR002320Thr-tRNA-ligase_IIaFamily
IPR004095TGSDomain
IPR004154Anticodon-bdDomain
IPR006195aa-tRNA-synth_IIDomain
IPR012675Beta-grasp_dom_sfHomologous_superfamily
IPR012676TGS-likeHomologous_superfamily
IPR012947tRNA_SADDomain
IPR018163Thr/Ala-tRNA-synth_IIc_editHomologous_superfamily
IPR033728ThrRS_coreDomain
IPR036621Anticodon-bd_dom_sfHomologous_superfamily
IPR045864aa-tRNA-synth_II/BPL/LPLHomologous_superfamily
IPR047246ThrRS_anticodonDomain

Pfam: PF00587, PF02824, PF03129, PF07973

Catalyzed reactions (Rhea)

  • tRNA(Thr) + L-threonine + ATP = L-threonyl-tRNA(Thr) + AMP + diphosphate + H(+) (RHEA:24624)

UniProt features (8 total): sequence conflict 2, transit peptide 1, chain 1, domain 1, modified residue 1, splice variant 1, sequence variant 1

Structure

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9BW92-F191.190.83

Human Protein Atlas

Protein class: Enzymes, ENZYME proteins, Ligase, Predicted intracellular proteins, Disease related genes, Potential drug targets, Human disease related genes, Congenital disorders of metabolism

Protein evidence: Evidence at protein level

Subcellular location (HPA, imaging): cytosol; nucleoplasm

Antibody reliability (HPA): IH approved · IF uncertain

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (1)

TypePositions
Phosphoserine52

Function

Pathways and Gene Ontology

Reactome pathways

0 curated (TAS) of 4; 0 disease pathways. Curated-first; evidence = TAS (manually curated) vs IEA (electronic inference).

4 pathways:

IDPathwayEvidence
R-HSA-392499Metabolism of proteins—
R-HSA-379726Mitochondrial tRNA aminoacylationelectronic
R-HSA-72766Translation—
R-HSA-379724tRNA Aminoacylation—

MSigDB gene sets: 229 (showing top): GSE45365_NK_CELL_VS_CD8_TCELL_DN, GOBP_AMINO_ACID_ACTIVATION, GOBP_TRNA_METABOLIC_PROCESS, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_DN, GOBP_MITOCHONDRIAL_TRANSLATION, GOBP_TRANSLATION, MARTIN_VIRAL_GPCR_SIGNALING_UP, GOBP_MITOCHONDRIAL_RNA_METABOLIC_PROCESS, KEGG_AMINOACYL_TRNA_BIOSYNTHESIS, KIM_GASTRIC_CANCER_CHEMOSENSITIVITY, GOBP_REGULATION_OF_TRANSLATIONAL_FIDELITY, REACTOME_MITOCHONDRIAL_TRNA_AMINOACYLATION, chr1q21, GOCC_MITOCHONDRIAL_MATRIX

GO Biological Process (6): threonyl-tRNA aminoacylation (GO:0006435), mitochondrial threonyl-tRNA aminoacylation (GO:0070159), translation (GO:0006412), tRNA aminoacylation for protein translation (GO:0006418), tRNA aminoacylation (GO:0043039), aminoacyl-tRNA metabolism involved in translational fidelity (GO:0106074)

GO Molecular Function (8): aminoacyl-tRNA deacylase activity (GO:0002161), threonine-tRNA ligase activity (GO:0004829), ATP binding (GO:0005524), protein homodimerization activity (GO:0042803), nucleotide binding (GO:0000166), aminoacyl-tRNA ligase activity (GO:0004812), protein binding (GO:0005515), ligase activity (GO:0016874)

GO Cellular Component (3): mitochondrion (GO:0005739), mitochondrial matrix (GO:0005759), cytoplasm (GO:0005737)

Reactome top-level categories

3 top-level categories:

CategoryPathways
tRNA Aminoacylation1
Translation1
Metabolism of proteins1

GO top-level categories

36 GO namespaces:

CategoryTerms
mitochondrion2
tRNA metabolic process2
catalytic activity, acting on a tRNA2
tRNA aminoacylation for protein translation1
threonyl-tRNA aminoacylation1
tRNA aminoacylation for mitochondrial protein translation1
peptidyltransferase activity1
translational initiation1
translational elongation1
translational termination1
macromolecule biosynthetic process1
protein metabolic process1
protein biosynthetic process1
translation1
tRNA aminoacylation1
amino acid activation1
regulation of translational fidelity1
carboxylic ester hydrolase activity1
aminoacyl-tRNA metabolism involved in translational fidelity1
deacylase activity1
aminoacyl-tRNA ligase activity1
adenyl ribonucleotide binding1
purine ribonucleoside triphosphate binding1
anion binding1
identical protein binding1
protein dimerization activity1
nucleoside phosphate binding1
heterocyclic compound binding1
ligase activity, forming carbon-oxygen bonds1
binding1
catalytic activity1
cytoplasm1
intracellular membrane-bounded organelle1
intracellular organelle lumen1
intracellular anatomical structure1
cellular anatomical structure1

Experimentally-supported GO annotations

GO terms backed by direct experimental evidence (ECO experimental codes) — 4 of 17 annotations. The rest are phylogenetic / computational / electronic (IEA).

4 experimentally-supported GO terms:

GO termNSEvidence
mitochondrionCChigh-throughput
aminoacyl-tRNA deacylase activityMFdirect assay
protein homodimerization activityMFdirect assay
threonine-tRNA ligase activityMFdirect assay

Protein interactions and networks

STRING

showing 15 of 1,284 interactions by confidence (×1000):

Protein AProtein BPartner UniProtScore
TARS2LARS2Q15031965
TARS2LARS1Q9P2J5951
TARS2AARS1P49588897
TARS2IARS2Q9NSE4882
TARS2IARS1P41252833
TARS2AARS2Q5JTZ9829
TARS2PARS2Q7L3T8816
TARS2YARS1P54577814
TARS2HARS1P12081808
TARS2YARS2Q9Y2Z4804
TARS2VARS2Q5ST30803
TARS2VARS1P26640797
TARS2HARS2P49590796
TARS2NARS2Q96I59794
TARS2MARS2Q96GW9792

IntAct

Human interaction partners of TARS2 in IntAct, one row per partner (best MIscore; records = supporting IntAct interaction records).

12 partners by confidence:

PartnerInteraction typeMIscoreRecords
ARL6IP1physical association0.5603
ASB6physical association0.5603
DDIT4Lphysical association0.5603
FKBP7physical association0.5603
MAL2physical association0.5603
PLIN3physical association0.5603
SFT2D1physical association0.5603
SLC17A9physical association0.5603
SYPL1physical association0.5603
TARS3physical association0.5603
TNFRSF10Dphysical association0.5603
EIF4A2physical association0.0001

BioGRID (184 interactions; top human partners by supporting records): AHSA1 (Affinity Capture-Luminescence; 2 records), CDC37 (Affinity Capture-Luminescence; 2 records), CHORDC1 (Affinity Capture-Luminescence; 2 records), CLPP (Proximity Label-MS; 2 records), CS (Proximity Label-MS; 2 records), CUL3 (Affinity Capture-MS; 2 records), EGFR (Affinity Capture-MS; 2 records), FKBPL (Affinity Capture-Luminescence; 2 records), PARK2 (Affinity Capture-MS; 2 records), AARS2 (Proximity Label-MS), ACE2 (Affinity Capture-MS), ACSM5 (Affinity Capture-MS), ADAM7 (Affinity Capture-MS), AIFM1 (Proximity Label-MS), AK4 (Affinity Capture-MS)

SIGNOR signaling

2 signaling interactions:

AEffectBMechanism
QRICH1“up-regulates quantity by expression”TARS2“transcriptional regulation”
ATF4“up-regulates quantity by expression”TARS2“transcriptional regulation”

Disease & clinical

Genetic variants

Variant evidence for TARS2: 352 ClinVar records (18 pathogenic / likely pathogenic); 17 GWAS associations. Per-variant detail is on Sugi Variant.

ClinVar

352 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic2
Likely pathogenic16
Uncertain significance135
Likely benign111
Benign50

Top pathogenic / likely-pathogenic (15)

Showing the 15 best-reviewed of 18 pathogenic / likely-pathogenic ClinVar records, ranked by ClinVar review status (expert panel → multiple submitters → single submitter), then by number of submitting labs.

Variant IDHGVSClassificationReviewSubmitters
1174007NM_025150.5(TARS2):c.1274A>G (p.Glu425Gly)Likely pathogeniccriteria provided, single submitter3
143049NM_025150.5(TARS2):c.845C>T (p.Pro282Leu)Likely pathogeniccriteria provided, single submitter2
1174009NM_025150.5(TARS2):c.1678G>C (p.Asp560His)Likely pathogeniccriteria provided, single submitter2
1341959NM_025150.5(TARS2):c.470C>G (p.Thr157Arg)Likely pathogeniccriteria provided, single submitter2
1341960NM_025150.5(TARS2):c.2143G>A (p.Glu715Lys)Likely pathogeniccriteria provided, single submitter2
432091NM_025150.5(TARS2):c.1756C>T (p.Arg586Ter)Likely pathogeniccriteria provided, single submitter1
2663569NM_025150.5(TARS2):c.191C>G (p.Ser64Ter)Likely pathogeniccriteria provided, single submitter1
3892600NM_025150.5(TARS2):c.996T>G (p.Tyr332Ter)Likely pathogeniccriteria provided, single submitter1
4072010NM_025150.5(TARS2):c.774G>T (p.Ser258=)Likely pathogeniccriteria provided, single submitter1
4072011NM_025150.5(TARS2):c.1099C>T (p.His367Tyr)Likely pathogeniccriteria provided, single submitter1
4845769NM_025150.5(TARS2):c.1037G>A (p.Arg346His)Likely pathogeniccriteria provided, single submitter1
3767312TARS2, 1-BP DUP, NT988Pathogenicno assertion criteria provided1
3767313R171KPathogenicno assertion criteria provided1
1992417NM_025150.5(TARS2):c.464C>T (p.Pro155Leu)Likely pathogenicno assertion criteria provided1
1992419NM_025150.5(TARS2):c.1318G>A (p.Glu440Lys)Likely pathogenicno assertion criteria provided1

Per-variant reference — Sugi Variant

Explore TARS2’s pathogenic and likely-pathogenic variants individually — each with its ClinVar classification and conditions, applied ACMG criteria (ClinGen expert panel, where curated), the calibrated in-silico predictors (AlphaMissense, REVEL, SaProt, conservation), gnomAD frequency, and the predictor-disagreement QC signal — on Sugi Variant.

SpliceAI

Top 10 splice-impact sites by Δscore (adjacent positions with the same effect merged into one range; 20 predictions of 1,519):

Position(s)EffectΔscoreSites
1:150488924acceptor_gain1.0000
1:150488942acceptor_gain1.0000
1:150488948acceptor_gain1.0000
1:150488955–150488956acceptor_gain1.00002
1:150488959acceptor_gain1.0000
1:150489088–150489089donor_loss1.00005
1:150491524donor_gain1.0000
1:150499035–150499036donor_loss1.00004
1:150499205acceptor_gain1.0000
1:150499213–150499215acceptor_gain1.00003

AlphaMissense

1,038 missense substitutions predicted likely pathogenic (of 4,613 scored), across 309 residues. Top 20 hotspot residues, ranked by the number of likely-pathogenic substitutions (of those reachable by a single-nucleotide change), then by mean score:

ResidueLikely-pathogenic substitutionsMean am_pathogenicityMax am_pathogenicity
D45780.9450.986
D56080.9290.964
D45880.9120.968
N40880.9020.989
H58580.8840.980
F56780.8830.973
H46080.8780.943
F45480.8670.965
F53580.8590.982
F43380.8530.966
F46280.8460.968
H36780.8400.958
H41280.8310.943
D43280.8260.929
D10680.7590.844
W36270.9490.983
F41670.9380.981
W50870.9300.974
F34870.9250.981
W61070.8870.973

HPA cancer prognostics

RNA cancer specificity: Low cancer specificity

Disease associations

OMIM: gene MIM:612805 | disease phenotypes: MIM:615918

GenCC curated gene-disease

1 curated gene-disease records:

DiseaseClassificationInheritanceRecords
combined oxidative phosphorylation defect type 21DefinitiveAutosomal recessive5

ClinGen Gene-Disease Validity

Expert-panel classifications — Definitive > Strong > Moderate > Limited > Disputed > Refuted.

2 validity classifications:

DiseaseClassificationInheritance
Leigh syndromeLimitedAR
mitochondrial diseaseDefinitiveAR

Genomics England panels (PanelApp)

Clinical diagnostic gene panels including this gene (11 panels, 10 green/diagnostic-grade). Confidence: green = diagnostic, amber = moderate.

11 panels:

PanelRating
Dystonia, chorea or related movement disorder, childhood onsetgreen
Early onset or syndromic epilepsygreen
Hypotonic infantgreen
Intellectual disabilitygreen
Leukodystrophy, childhood onsetgreen
Likely inborn error of metabolismgreen
Mitochondrial disordersgreen
Paediatric disordersgreen
Possible mitochondrial disorder, nuclear genesgreen
Unexplained death in infancy and sudden unexplained death in childhoodgreen
Neonatal diabetesamber

Mondo (1): combined oxidative phosphorylation defect type 21 (MONDO:0014398)

Orphanet (1): Combined oxidative phosphorylation defect type 21 (Orphanet:420733)

HPO phenotypes

16 phenotypes (HPO-id order):

HPOTerm
HP:0000007Autosomal recessive inheritance
HP:0000817Reduced eye contact
HP:0001250Seizure
HP:0001263Global developmental delay
HP:0001397Hepatic steatosis
HP:0002059Cerebral atrophy
HP:0002079Hypoplasia of the corpus callosum
HP:0002151Increased circulating lactate concentration
HP:0002509Limb hypertonia
HP:0003348Hyperalaninemia
HP:0003577Congenital onset
HP:0003593Infantile onset
HP:0003811Neonatal death
HP:0008358Hyperprolinemia
HP:0008936Axial hypotonia
HP:0011813Increased cerebral lipofuscin

GWAS associations

17 associations:

StudyTraitp-value
GCST010700_28Cortical thickness (MOSTest)8e-38
GCST007565_182Morning person6e-30
GCST007576_401Chronotype6e-30
GCST90002400_128Plateletcrit3e-24
GCST010696_2Cortical thickness (min-P)2e-23
GCST90013405_109Liver enzyme levels (alanine transaminase)2e-20
GCST003837_3Chronotype6e-17
GCST010002_27Refractive error3e-15
GCST90011898_2Alanine aminotransferase levels1e-12
GCST010701_57Cortical surface area (MOSTest)9e-12
GCST010703_294Brain morphology (MOSTest)9e-12
GCST010702_101Subcortical volume (MOSTest)4e-9
GCST010697_28Cortical surface area (min-P)9e-9
GCST010698_54Subcortical volume (min-P)2e-8
GCST010699_28Brain morphology (min-P)3e-8
GCST010245_43LDL cholesterol levels4e-8
GCST003838_10Morning vs. evening chronotype5e-7

EFO canonical traits (from GWAS)

5 canonical traits:

EFO IDTrait name
EFO:0008328chronotype measurement
EFO:0004611low density lipoprotein cholesterol measurement
EFO:0004346neuroimaging measurement
EFO:0004840cortical thickness
EFO:0007985platelet crit

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL3351186 (SINGLE PROTEIN)

PharmGKB: 1 entry (CPIC guideline: no)

Binding affinities (BindingDB)

1 measured of 1 human assays (1 total across all organisms); most potent 1 below. Values come from heterogeneous assays and are not directly comparable.

LigandMeasureValue
CHEMBL5653589KD1440 nM

ChEMBL bioactivities

2 potent at pChembl≥5 of 2 total, top 2 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChemblTypeValueUnitMolecule
8.23Kd5.919nMCHEMBL5653589
8.23ED505.919nMCHEMBL5653589

PubChem BioAssay actives

1 with measured affinity, of 4 total; 1 most potent distinct compounds. Largely complementary to BindingDB; screening values are coarse (µM, 4 dp), so sub-nM hits tie at the floor.

CompoundAssayTypeValueUnit
4-methyl-3-[(2-methyl-6-pyridin-3-ylpyrazolo[3,4-d]pyrimidin-4-yl)amino]-N-[3-(trifluoromethyl)phenyl]benzamide2149549: Binding affinity to human TARS2 incubated for 45 mins by Kinobead based pull down assaykd0.0059uM

CTD chemical–gene interactions

24 total (human), top 24 by PubMed support.

ChemicalActions (top 5)PubMed papers
Acetaminophenaffects cotreatment, decreases expression2
Cadmium Chloridedecreases expression2
bisphenol Adecreases expression1
sodium arsenitedecreases expression1
potassium chromate(VI)affects cotreatment, decreases expression1
gossypol acetic aciddecreases expression1
2,3-bis(3’-hydroxybenzyl)butyrolactoneincreases expression, affects cotreatment1
aflatoxin B2increases methylation1
epigallocatechin gallateaffects cotreatment, decreases expression1
di-n-butylphosphoric acidaffects expression1
Benzo(a)pyreneaffects methylation1
Carbamazepineaffects expression1
Coumestrolincreases expression, affects cotreatment1
Hydrogen Peroxideaffects cotreatment, decreases expression1
Lipopolysaccharidesaffects cotreatment, decreases expression1
Phenobarbitalaffects expression1
Potassium Dichromatedecreases expression1
Theophyllineaffects cotreatment, decreases expression1
Thiramdecreases expression1
Tobacco Smoke Pollutiondecreases expression1
Cyclosporinedecreases expression1
Aflatoxin B1increases methylation1
Copper Sulfatedecreases expression1
Lactic Aciddecreases expression1

ChEMBL screening assays

2 unique, capped per target: 2 binding

Representative assays (with source publication via chembl_document):

Assay IDTypeDescriptionSource paper
CHEMBL3383853BindingInhibition of threonyl tRNA synthetase (unknown origin) assessed as depletion of tRNAs at 50 uM by SToPs assayBorrelidin B: isolation, biological activity, and implications for nitrile biosynthesis. — *J Nat Prod*

Cellosaurus cell lines

1 cell lines: 1 cancer cell line

First 10 cell lines (id-ordered, not curated):

CellosaurusNameCategorySex
CVCL_E0QJUbigene HeLa TARS2 KOCancer cell lineFemale

Clinical trials (associated diseases)

Via MONDO — disease-level, not drug-specific.

showing 60 of 210 trials:

NCTPhaseStatusTitle
NCT04586348Phase 4UNKNOWNPrenatal Iodine Supplementation and Early Childhood Neurodevelopment
NCT04873115Phase 4UNKNOWNDouble-blind, Placebo-controlled, Randomized Clinical Trial Comparing the Efficacy and Safety of Sialanar Plus orAl rehabiLitation Against Placebo Plus Oral Rehabilitation for chIldren and Adolescents With seVere Sialorrhoea and Neurodisabilties,
NCT02559102Phase 3COMPLETEDDexmedetomidine Sedation Versus General Anaesthesia for Inguinal Hernia Surgery in Infants
NCT02757079Phase 3COMPLETEDStudy of the Efficacy and Safety of NPC-15 for Sleep Disorders of Children With Neurodevelopmental Disorders
NCT06915480Phase 3RECRUITINGReducing Missed Appointments
NCT07377032Phase 3RECRUITINGTAP-GRIN: Interventional Study on Patients With GRIN-related Neurodevelopmental Disorders
NCT02909959Phase 2COMPLETEDSulforaphane for the Treatment of Young Men With Autism Spectrum Disorder
NCT06081348Phase 2RECRUITINGSertraline vs. Placebo in the Treatment of Anxiety in Children and AdoLescents With NeurodevelopMental Disorders
NCT06352372Phase 2COMPLETEDSafety and Efficacy of tPBM for Epileptiform Activity in Autism
NCT00503191Phase 1COMPLETEDNeuroModulation Technique Treatment of Autism
NCT04475848Phase 1COMPLETEDA Study to Investigate the Safety, Tolerability, Pharmacokinetics, Pharmacodynamics and Food Effect of RO6953958 in Healthy Participants
NCT06300398Phase 1COMPLETEDIAMA-6 Oral Dose Study in Healthy Adults
NCT01783041Phase 2/3COMPLETEDEffect of Early L-Carnitine Supplementation on Neurodevelopmental Outcomes in Very Preterm Infants
NCT05767385Phase 2/3COMPLETEDFetal Cerebrovascular Autoregulation in Congenital Heart Disease and Association With Neonatal Neurobehavior
NCT05675098Early Phase 1NOT_YET_RECRUITINGCentral Nervous System Stimulants and Physical Function in Children With Cerebral Palsy
NCT00783783Not specifiedCOMPLETEDCYP2D6 Pharmacogenetics in Risperidone-Treated Children
NCT01778504Not specifiedRECRUITINGStudying Childhood-onset Behavioral, Psychiatric, and Developmental Disorders
NCT01850784Not specifiedUNKNOWNHigh Energy Formula Feeding in Infants With Congenital Heart Disease
NCT01922791Not specifiedCOMPLETEDNutrition and Pregnancy Intervention Study
NCT01942525Not specifiedUNKNOWNInfluence of Intrauterine Growth Restriction on Amplitude-integrated EEG in Preterm Infants
NCT02003170Not specifiedCOMPLETEDEtiology and Early Diagnosis of Neurodevelopmental Disorders
NCT02118649Not specifiedCOMPLETEDEnhancing Behavior and Brain Response to Visual Targets Using a Computer Game
NCT02557191Not specifiedTERMINATEDBiomarkers, Neurodevelopment and Preterm Infants
NCT02690675Not specifiedCOMPLETEDIron Supplement Effect on Child Development
NCT02694003Not specifiedCOMPLETEDBetter Nights, Better Days for Children With Neurodevelopment Disorders
NCT02792894Not specifiedCOMPLETEDFamily Networks (FaNs) for Children With Developmental Disorders and Delays
NCT02871674Not specifiedUNKNOWNGood Night Project: Behavioural Sleep Interventions for Children With ADHD: A Randomised Controlled Trial
NCT02887157Not specifiedCOMPLETEDAnalyzing Retinal Microanatomy in ROP
NCT02898298Not specifiedCOMPLETEDPositive Emotion Regulation Training in Children, Adolescents and Young Adults With and Without Developmental Disorder
NCT02912780Not specifiedUNKNOWNIntroduction of Microsystems in a Level 3 Neonatal Intensive Care Unit
NCT03023293Not specifiedCOMPLETEDn-3 PUFAs, Irisin and Maternal Glucose Metabolism From Pregnancy to Postpartum
NCT03023644Not specifiedCOMPLETEDImproving Neurodevelopmental Outcomes in Children With Congenital Heart Disease: An Intervention Study
NCT03032991Not specifiedUNKNOWNEarly Biomarkers of Neurodevelopment in Offspring of Diabetic Mothers
NCT03088189Not specifiedTERMINATEDEffect of Parental Peri-conceptional Vitamin B12 Supplementation on Infant Neurocognitive Development in Offspring
NCT03096028Not specifiedCOMPLETEDDevelopmental Origins of Mental Health Disorders
NCT03148782Not specifiedCOMPLETEDBrain Plasticity Underlying Acquisition of New Organizational Skills in Children-R61 Phase
NCT03172104Not specifiedCOMPLETEDNeurobehavioural Development of Infants Born <30 Weeks Gestational Age Between Birth and Five Years of Age
NCT03222375Not specifiedRECRUITINGSQUED™ Series 28.1 Home-use and Treatment of Autowave Reverberator of Autism
NCT03229928Not specifiedCOMPLETEDClinical Testing of a Real-Time Behavior Measurement Tool: Measuring Outcomes for CHAnge
NCT03232489Not specifiedUNKNOWNStudy for the Evaluation of the Feasibility of Applying Advanced MRI Scanning in Pediatric Clinical Practice
NCT03381027Not specifiedCOMPLETEDBABY SMART (Study of Massage Therapy, Sleep And neurodevelopMenT)
NCT03388294Not specifiedCOMPLETEDEvaluation of a Novel Intervention for Infants At Risk for Neurodevelopmental Disorders
NCT03410810Not specifiedUNKNOWNChildhood Outcomes of Preterm Brain Abnormalities
NCT03492060Not specifiedRECRUITINGLongitudinal Study of Neurogenetic Disorders
NCT03577756Not specifiedCOMPLETEDNeurodevelopmental Assessment of Infants With Cystic Fibrosis
NCT03654248Not specifiedCOMPLETEDLet’s Get Organized in Adult Psychiatric/habilitation Care
NCT03659279Not specifiedCOMPLETEDLet’s Get Organized Feasibility Study
NCT03722615Not specifiedCOMPLETEDEpidemiology of Congenital Cytomegalovirus in a High HIV Prevalence Setting, South Africa
NCT03770832Not specifiedACTIVE_NOT_RECRUITINGWearable Sensors and Video Recordings to Monitor Motor Development
NCT03830879Not specifiedRECRUITINGShenzhen Birth Cohort Study
NCT03835689Not specifiedCOMPLETEDStrongest FamiliesTM Neurodevelopmental
NCT03882788Not specifiedCOMPLETEDThe Effect of Anesthesia on Neurodevelopmental Outcome (NDO)
NCT03922087Not specifiedCOMPLETEDNo-worry Baby Project
NCT03977259Not specifiedACTIVE_NOT_RECRUITINGTargeting Human Milk Fortification to Improve Preterm Infant Growth and Brain Development
NCT04043572Not specifiedUNKNOWNThe Biomarkers of Neurological Disease in Utero Study
NCT04096430Not specifiedRECRUITINGEvaluation of Effectiveness of Child-oriented Goal-setting in Paediatric Rehabilitation (the ENGAGE Approach)
NCT04108273Not specifiedCOMPLETEDBrain Plasticity Underlying Acquisition of New Organizational Skills in Children
NCT04201509Not specifiedCOMPLETEDValidity of Neurocognitive Assessment Methods in Childhood ADHD
NCT04233775Not specifiedUNKNOWNAltered Cerebral Growth and Development in Infants With Congenital Heart Disease
NCT04313283Not specifiedCOMPLETEDTranslating Peer-to-Peer Support Into a Clinical Setting

Predicted chemistry — Sugi Predict

The predicted patent-compound landscape for TARS2 across ~30M SureChEMBL compounds — explore on Sugi Predict.