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LARS1

gene
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Also known as HSPC192FLJ10595FLJ21788LEUSRNTLS

Summary

LARS1 (leucyl-tRNA synthetase 1, HGNC:6512) is a protein-coding gene on chromosome 5q32, encoding Leucine–tRNA ligase, cytoplasmic (Q9P2J5). Aminoacyl-tRNA synthetase that catalyzes the specific attachment of leucine to its cognate tRNA (tRNA(Leu)). It is a common-essential gene (DepMap: required in 99.5% of cancer cell lines).

This gene encodes a cytosolic leucine-tRNA synthetase, a member of the class I aminoacyl-tRNA synthetase family. The encoded enzyme catalyzes the ATP-dependent ligation of L-leucine to tRNA(Leu). It is found in the cytoplasm as part of a multisynthetase complex and interacts with the arginine tRNA synthetase through its C-terminal domain. A mutation in this gene was found in affected individuals with infantile liver failure syndrome 1. Alternatively spliced transcript variants of this gene have been observed.

Source: NCBI Gene 51520 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): infantile liver failure syndrome 1 (Strong, GenCC)
  • Clinical variants (ClinVar): 605 total — 14 pathogenic, 14 likely-pathogenic (top 6% of genes corpus-wide)
  • GTEx eGene: eQTL in 49 tissues, sQTL in 47 (q < 0.05)
  • Phenotypes (HPO): 21
  • Cancer dependency (DepMap): dependent in 99.5% of screened cell lines (common-essential)
  • Constraint (gnomAD): pLI 0.00 (LoF-tolerant), LOEUF 0.79 (unconstrained)
  • MANE Select transcript: NM_020117
  • Interaction hub: 2,395 STRING partners (top 5% of genes corpus-wide)

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:6512
Approved symbolLARS1
Nameleucyl-tRNA synthetase 1
Location5q32
Locus typegene with protein product
StatusApproved
AliasesHSPC192, FLJ10595, FLJ21788, LEUS, RNTLS
Ensembl geneENSG00000133706
Ensembl biotypeprotein_coding
OMIM151350
Entrez51520

Gene structure

Transcript identifiers

Ensembl transcripts: 64 — 31 protein_coding, 17 nonsense_mediated_decay, 13 retained_intron, 3 protein_coding_CDS_not_defined

MANE Select: ENST00000394434

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

ENST00000394434, ENST00000504323, ENST00000505223, ENST00000506231, ENST00000507095, ENST00000508667, ENST00000508709, ENST00000510191, ENST00000511505, ENST00000512412, ENST00000618084, ENST00000674158, ENST00000674170, ENST00000674174, ENST00000674181, ENST00000674191, ENST00000674218, ENST00000674270, ENST00000674277, ENST00000674290, ENST00000674309, ENST00000674310, ENST00000674383, ENST00000674398, ENST00000674412, ENST00000674417, ENST00000674447, ENST00000674450, ENST00000674467, ENST00000674471, ENST00000674479, ENST00000907998, ENST00000907999, ENST00000908000, ENST00000908001, ENST00000908002, ENST00000908003, ENST00000908004, ENST00000923242, ENST00000923243, ENST00000923244, ENST00000923245, ENST00000923246, ENST00000923247, ENST00000923248, ENST00000923249, ENST00000970933, ENST00000970934, ENST00001003405, ENST00001003406, ENST00001003407, ENST00001043438, ENST00001043441, ENST00001043442, ENST00001080414, ENST00001080415, ENST00001080416, ENST00001080417, ENST00001080420, ENST00001080421, ENST00001103876, ENST00001107682, ENST00001130428, ENST00001139101

RefSeq mRNA: 4 — MANE Select: NM_020117 NM_001317964, NM_001317965, NM_016460, NM_020117

CCDS: CCDS34265, CCDS83029, CCDS93797, CCDS93798

Canonical transcript exons

ENST00000394434 — 32 exons

ExonStartEnd
ENSE00001026660146153893146153980
ENSE00001026662146157403146157628
ENSE00001026664146131019146131109
ENSE00001026669146153174146153227
ENSE00001026689146151862146152002
ENSE00001026692146153734146153810
ENSE00001156449146132898146133081
ENSE00001752781146182488146182650
ENSE00002465699146130018146130158
ENSE00002505955146113034146114311
ENSE00003471443146128672146128782
ENSE00003488127146126435146126545
ENSE00003492300146123982146124086
ENSE00003509120146177547146177665
ENSE00003509134146120371146120503
ENSE00003512870146144624146144709
ENSE00003536965146157728146157795
ENSE00003544811146168128146168265
ENSE00003548361146135601146135664
ENSE00003566597146164310146164471
ENSE00003567194146159407146159470
ENSE00003568827146143412146143550
ENSE00003569000146144267146144349
ENSE00003589329146149622146149699
ENSE00003609043146171910146171990
ENSE00003611362146142872146143084
ENSE00003618671146128978146129118
ENSE00003639628146160374146160486
ENSE00003643699146144472146144537
ENSE00003643724146140204146140261
ENSE00003656293146172687146172774
ENSE00003666274146122492146122587

Expression profiles

Bgee: expression breadth ubiquitous, 292 present calls, max score 97.76.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 82.7100 / max 2081.2741, expressed in 1819 samples.

Highest expression (Bgee): Brodmann (1909) area 23, endothelial cell, ventricular zone, adrenal tissue, middle temporal gyrus.

Genetic regulation across tissues (GTEx eQTL / sQTL)

LARS1 is an eGene in GTEx v10 — its expression is genetically regulated (eQTL) in 49 tissues and its splicing (sQTL) in 47 (q < 0.05). Strongest associations first; slope = normalized effect of the lead variant’s alternative allele.

showing 20 of 96 significant tissue × QTL associations:

TissueQTLq-valueSlopeLead variant
Thyroideqtl1.1e-118+0.855:146092836:G:A
Nerve Tibialeqtl6.8e-101+0.535:146153364:T:C
Artery Tibialeqtl8.1e-77+0.485:146135783:C:T
Adipose Subcutaneouseqtl9.5e-73+0.425:146100495:C:CATT
Breast Mammary Tissueeqtl1.4e-64+0.525:146094254:G:A
Esophagus Musculariseqtl1.3e-62+0.475:146126685:C:T
Cells Cultured fibroblastseqtl3.7e-62+0.325:146177423:G:A
Adipose Visceral Omentumeqtl5.4e-62+0.435:146165203:A:G
Artery Aortaeqtl2.1e-60+0.675:146125921:T:G
Lungeqtl2.6e-56+0.365:146092836:G:A
Skin Sun Exposed Lower legeqtl3.2e-53+0.405:146135783:C:T
Esophagus Mucosaeqtl3.9e-53+0.345:146176249:C:T
Colon Transverseeqtl8.6e-51+0.715:146126196:A:G
Skin Not Sun Exposed Suprapubiceqtl1.8e-50+0.475:146126196:A:G
Esophagus Gastroesophageal Junctioneqtl6.0e-47+0.525:146127039:G:A
Muscle Skeletalsqtl1.8e-46+1.035:146084032:T:C
Skin Sun Exposed Lower legsqtl2.7e-46+1.035:146135783:C:T
Adipose Subcutaneoussqtl9.5e-44-1.045:146173839:G:C
Pancreaseqtl1.8e-43+0.685:146153364:T:C
Brain Cerebellumeqtl5.9e-41+0.845:146135783:C:T

FANTOM5 promoters

4 alternative TSS:

Promoter IDTPM avgSamples expressed
6398877.64661819
639862.97211141
639871.2529632
639850.8383311

Top tissues by expression

showing 100 of 296 tissues by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
Brodmann (1909) area 23UBERON:001355497.76gold quality
endothelial cellCL:000011597.43silver quality
ventricular zoneUBERON:000305397.33gold quality
adrenal tissueUBERON:001830396.92gold quality
middle temporal gyrusUBERON:000277196.86gold quality
body of pancreasUBERON:000115096.76gold quality
right uterine tubeUBERON:000130296.52gold quality
ganglionic eminenceUBERON:000402396.49gold quality
primary visual cortexUBERON:000243696.21gold quality
cartilage tissueUBERON:000241896.14gold quality
pancreasUBERON:000126496.03gold quality
islet of LangerhansUBERON:000000695.85gold quality
colonic epitheliumUBERON:000039795.85gold quality
tonsilUBERON:000237295.80gold quality
mucosa of paranasal sinusUBERON:000503095.68gold quality
gastrocnemiusUBERON:000138895.65gold quality
cortical plateUBERON:000534395.65gold quality
stromal cell of endometriumCL:000225595.51gold quality
muscle of legUBERON:000138395.46gold quality
corpus callosumUBERON:000233695.39gold quality
germinal epithelium of ovaryUBERON:000130495.36gold quality
medial globus pallidusUBERON:000247795.36gold quality
endometriumUBERON:000129595.30gold quality
cerebellar cortexUBERON:000212995.24gold quality
cerebellar hemisphereUBERON:000224595.23gold quality
tendon of biceps brachiiUBERON:000818895.20gold quality
right lobe of thyroid glandUBERON:000111995.08gold quality
superficial temporal arteryUBERON:000161495.08gold quality
cerebellumUBERON:000203794.98gold quality
heart right ventricleUBERON:000208094.97gold quality
right ovaryUBERON:000211894.94gold quality
right hemisphere of cerebellumUBERON:001489094.92gold quality
right adrenal gland cortexUBERON:003582794.90gold quality
rectumUBERON:000105294.84gold quality
skeletal muscle organUBERON:001489294.78gold quality
muscle organUBERON:000163094.77gold quality
tendonUBERON:000004394.76gold quality
right adrenal glandUBERON:000123394.75gold quality
calcaneal tendonUBERON:000370194.74gold quality
gingival epitheliumUBERON:000194994.66gold quality
adrenal glandUBERON:000236994.63gold quality
occipital lobeUBERON:000202194.61gold quality
gingivaUBERON:000182894.58gold quality
globus pallidusUBERON:000187594.56gold quality
left ovaryUBERON:000211994.53gold quality
body of uterusUBERON:000985394.53gold quality
minor salivary glandUBERON:000183094.51gold quality
thyroid glandUBERON:000204694.50gold quality
hindlimb stylopod muscleUBERON:000425294.49gold quality
right coronary arteryUBERON:000162594.48gold quality
entorhinal cortexUBERON:000272894.45gold quality
left adrenal glandUBERON:000123494.44gold quality
adrenal cortexUBERON:000123594.41gold quality
left lobe of thyroid glandUBERON:000112094.38gold quality
mouth mucosaUBERON:000372994.37gold quality
left adrenal gland cortexUBERON:003582594.37gold quality
embryoUBERON:000092294.36gold quality
cardia of stomachUBERON:000116294.36gold quality
skin of hipUBERON:000155494.36gold quality
smooth muscle tissueUBERON:000113594.35gold quality
pituitary glandUBERON:000000794.34gold quality
saliva-secreting glandUBERON:000104494.30gold quality
biceps brachiiUBERON:000150794.30gold quality
ovaryUBERON:000099294.28gold quality
uterusUBERON:000099594.28gold quality
adenohypophysisUBERON:000219694.23gold quality
superior frontal gyrusUBERON:000266194.20gold quality
left uterine tubeUBERON:000130394.19gold quality
postcentral gyrusUBERON:000258194.19gold quality
muscle layer of sigmoid colonUBERON:003580594.17gold quality
caudate nucleusUBERON:000187394.14gold quality
cardiac ventricleUBERON:000208294.12gold quality
heart left ventricleUBERON:000208494.12gold quality
dorsolateral prefrontal cortexUBERON:000983494.10gold quality
lower esophagus muscularis layerUBERON:003583394.04gold quality
lower esophagusUBERON:001347394.03gold quality
right frontal lobeUBERON:000281094.02gold quality
deltoidUBERON:000147694.01silver quality
right atrium auricular regionUBERON:000663194.00gold quality
endocervixUBERON:000045893.99gold quality
esophagogastric junction muscularis propriaUBERON:003584193.95gold quality
cauda epididymisUBERON:000436093.94gold quality
peritoneumUBERON:000235893.93gold quality
omental fat padUBERON:001041493.93gold quality
left coronary arteryUBERON:000162693.90gold quality
heartUBERON:000094893.87gold quality
coronary arteryUBERON:000162193.85gold quality
renal medullaUBERON:000036293.82gold quality
mucosa of sigmoid colonUBERON:000499393.82gold quality
cerebral cortexUBERON:000095693.80gold quality
Ammon’s hornUBERON:000195493.80gold quality
oral cavityUBERON:000016793.76gold quality
esophagusUBERON:000104393.76gold quality
adipose tissue of abdominal regionUBERON:000780893.75gold quality
anterior cingulate cortexUBERON:000983593.75gold quality
telencephalonUBERON:000189393.74gold quality
female reproductive systemUBERON:000047493.73gold quality
brainUBERON:000095593.73gold quality
cingulate cortexUBERON:000302793.73gold quality
forebrainUBERON:000189093.71gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-ANND-3yes9.62
E-GEOD-124858no676.35
E-MTAB-9689no389.19

HPA expression

RNA tissue specificity: Low tissue specificity

showing 60 of 78 HPA tissues / cells by nTPM:

Tissue / cellAxisnTPMProtein (IHC)
Tonguetissue54.9
Skeletal muscletissue51.4medium
Breasttissue43.3high
Cerebral cortextissue41.5high
Somatosensory cortextissue41.5
Occipital cortextissue40.9
Putamentissue39.8
Cerebellumtissue39.8medium
Retrosplenial and cingulate cortextissue39.7
Hippocampal formationtissue39.0
Entorhinal cortextissue39.0
Motor cortextissue38.3
Temporal cortextissue38.2
Retrosplenial cortextissue37.8
Salivary glandtissue37.7high
Prefrontal cortextissue37.5
Ponstissue37.0
Thalamustissue36.5
Midbraintissue36.3
Superior colliculitissue36.3
Insular cortextissue36.1
Basal gangliatissue35.7medium
Ventral forebraintissue35.6
Corpus callosumtissue35.4
Periaqueductal graytissue35.3
Olfactory bulbtissue34.9
Septumtissue34.7
Hypothalamustissue34.6
Substantia nigratissue34.5
Medulla oblongatatissue34.3
Amygdalatissue33.8
Epididymistissue33.4high
Rectumtissue32.7medium
Parathyroid glandtissue32.7medium
Tonsiltissue32.6medium
Thyroid glandtissue32.5medium
Spinal cordtissue32.5
Retinatissue32.2
Pituitary glandtissue31.5
Smooth muscletissue31.2medium
Thymustissue30.5
Kidneytissue30.1high
Ovarytissue29.5not detected
Endometrium 1tissue29.3high
Pancreastissue29.2medium
Colontissue28.7medium
Prostatetissue28.7high
Lymph nodetissue27.8not detected
Urinary bladdertissue27.8high
Fallopian tubetissue27.8high
Choroid plexustissue27.5
Vaginatissue26.9medium
Cervixtissue26.8medium
Heart muscletissue26.8medium
Seminal vesicletissue26.6high
Adrenal glandtissue26.6not detected
Appendixtissue25.1medium
Adipose tissuetissue25.0not detected
Spleentissue24.4low
Stomach 1tissue23.3medium

Brain sub-regions (HPA Brain Atlas): detected in 191; highest nTPM — Dorsal hippocampus (38.7), Ventral hippocampus (37.3), Subiculum (36.4), White matter (35.4), Dorsal spinal cord (32.5).

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): ATF4

miRNA regulators (miRDB)

Targeting LARS1 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific).

showing 30 of 63 miRNAs:

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-432-3P100.0067.86705
HSA-MIR-1193100.0065.93529
HSA-MIR-98-3P100.0074.083907
HSA-MIR-3134100.0066.43777
HSA-MIR-3646100.0073.565283
HSA-LET-7A-3P100.0074.033932
HSA-LET-7B-3P100.0074.083913
HSA-LET-7F-1-3P100.0074.023928
HSA-MIR-3163100.0077.238605
HSA-MIR-453499.9966.581907
HSA-MIR-150-5P99.9966.691976
HSA-MIR-569699.9872.364487
HSA-MIR-1213699.9872.815713
HSA-MIR-9-3P99.9670.882068
HSA-MIR-568099.9169.833421
HSA-MIR-548D-3P99.8770.674362
HSA-MIR-10395-5P99.8667.35676
HSA-MIR-548BB-3P99.8670.584354
HSA-MIR-5003-3P99.8569.292517
HSA-MIR-659-3P99.8570.691620
HSA-MIR-548AC99.8470.774351
HSA-MIR-548H-3P99.8470.804349
HSA-MIR-548Z99.8470.804349
HSA-MIR-6515-3P99.8268.191933
HSA-MIR-4668-5P99.7970.583782
HSA-MIR-320A-3P99.7769.732107
HSA-MIR-320B99.7769.732107
HSA-MIR-320C99.7769.732107
HSA-MIR-320D99.7769.732107
HSA-MIR-442999.7769.622111

Functional genomics

gnomAD constraint: pLI 1.15e-13, LOEUF 0.787, missense Z 1.62 — population loss-of-function intolerance (pLI ≥ 0.9 = LoF-intolerant; lower LOEUF = more constrained). gnomAD

Regional missense constraint (gnomAD RMC): no regional variation along ENST00000394434 — one region, missense o/e 0.89. DepMap (CRISPR cell-line fitness): dependent in 99.5% of screened cell lines, common-essential.

Most-dependent cell lines (DepMap gene-effect, lower = stronger; ≤ −0.5 shown): HCC38 (-2.229), HCC1187 (-2.202), MFE-280 (-2.068), Caov-4 (-2.03), KU812 (-2.029), UACC-62 (-1.959), Saos-2 (-1.934), S-117 (-1.825), HT-144 (-1.815), T24 (-1.758), JH-EsoAd1 (-1.753), TALL-1 (-1.749), SKM-1 (-1.749), RT4 (-1.734), MPP 89 (-1.733).

Literature-anchored findings (GeneRIF, showing 22)

  • leucyl-tRNA synthetase requires its C-terminal domain for its interaction with arginyl-tRNA synthetase in the multi-tRNA synthetase complex (PMID:16055448)
  • We identified a novel G3283A transition in the mitochondrial DNA tRNA(Leu (UUR)) gene in a patient with ptosis, ophthalmoparesis and hyporeflexia. (PMID:17363246)
  • Results show that K600 in human leucyl-tRNA synthetase affects amino acid specificity and tRNA aminoacylation. (PMID:17378584)
  • findings suggest that LARS1 may play roles in migration and growth of lung cancer cells, which suggest its potential implication in lung tumorigenesis (PMID:18446061)
  • Study of crystal structures of the editing domain from 2 eukaryotic cytosolic LeuRS; shows a conserved structural core containing the active site for hydrolysis, with distinct bacterial, archeal, or eukaryotic peripheral insertions. (PMID:19426743)
  • the introduction of bulky residues into the amino acid binding pocket failed to block deacylation of tRNA, indicating that the architecture of the amino acid binding pocket is different compared to that of other characterized LeuRSs (PMID:19702327)
  • hcLeuRS can charge RNALeu with non-cognate amino acids and exclude the incorrect products by multiple editing pathways. (PMID:20805241)
  • This work demonstrates that LRS is a key mediator for amino acid signaling to mTORC1. (PMID:22424946)
  • Identification of a mutation in LARS as a novel cause of infantile hepatopathy (PMID:22607940)
  • the carboxy-terminal domain of human mitochondrial (mt) leucyl-tRNA synthetase can be used to correct mt dysfunctions caused by mt-tRNA mutations. (PMID:24413190)
  • Lack of a CP1 hairpin in LeuRS led to complete loss of aminoacylation, amino acid activation, and tRNA binding; however, the mutants retained post-transfer editing. (PMID:25051973)
  • the KMSKS catalytic loop affects the aminoacylation and editing capacities of leucyl-tRNA synthetase (PMID:25817995)
  • The results showed a decrease in autophagy on addition of leucine, demonstrating crosstalk between leucine sensing, LRS translocation, RagD interaction, and mTORC1 activation. (PMID:28882589)
  • Leucyl-tRNA synthetase (LRS) is a leucine sensor of the mTORC1 pathway. (PMID:28963468)
  • this study provides evidence for a role of leucyl-tRNA synthetase 1 (LARS1) in glucose-dependent control of leucine usage. (PMID:31780625)
  • Molecular basis of the multifaceted functions of human leucyl-tRNA synthetase in protein synthesis and beyond. (PMID:32232361)
  • Genotypic diversity and phenotypic spectrum of infantile liver failure syndrome type 1 due to variants in LARS1. (PMID:32699352)
  • Severe course with lethal hepatocellular injury and skeletal muscular dysgenesis in a neonate with infantile liver failure syndrome type 1 caused by novel LARS1 mutations. (PMID:33300650)
  • Infantile Liver Failure Syndrome 1 associated with a novel variant of the LARS1 gene: Clinical, genetic, and functional characterization. (PMID:33314043)
  • Leucyl-tRNA synthetase 1 is required for proliferation of TSC-null cells. (PMID:34325132)
  • O-GlcNAc modification of leucyl-tRNA synthetase 1 integrates leucine and glucose availability to regulate mTORC1 and the metabolic fate of leucine. (PMID:35614056)
  • Identification of LARS as an essential gene for osteosarcoma proliferation through large-Scale CRISPR-Cas9 screening database and experimental verification. (PMID:35962451)

Cross-species orthologs

6 orthologs

OrganismSymbolGene ID
danio_reriolars1bENSDARG00000019280
danio_reriolars1aENSDARG00000090988
mus_musculusLars1ENSMUSG00000024493
rattus_norvegicusLars1ENSRNOG00000018304
drosophila_melanogasterLeuRSFBGN0284253
caenorhabditis_elegansWBGENE00003073

Paralogs (7): LARS2 (ENSG00000011376), IARS2 (ENSG00000067704), VARS2 (ENSG00000137411), MARS1 (ENSG00000166986), IARS1 (ENSG00000196305), VARS1 (ENSG00000204394), MARS2 (ENSG00000247626)

Mouse-model phenotypes

Observed phenotypes of the mouse ortholog (MGI:1913808) from MGI (Alliance of Genome Resources) — knockout/mutant phenotypes, ranked by annotation count. 1 distinct phenotype terms.

Mouse phenotype (MP)Records
preweaning lethality, complete penetrance1

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
Pongo abeliiQ5R61498.6%Diamond
Methanococcus maripaludis C5A4FYA396.2%Diamond
Methanococcus maripaludis S2Q6LZD295.4%Diamond
Thermococcus onnurineus NA1B6YST993.1%Diamond
Thermococcus kodakarensis KOD1Q8NKR793.1%Diamond
Pyrococcus horikoshii OT3O5869891.2%Diamond
Pyrococcus abyssi GE5Q9V0B991.2%Diamond
Pyrococcus furiosus DSM 3638Q8U2E691.0%Diamond
Pyrobaculum islandicum DSM 4184A1RTX986.8%Diamond
Pyrobaculum neutrophilum V24StaB1YAS986.8%Diamond
Pyrobaculum arsenaticum DSM 13514A4WHK682.8%Diamond
Pyrobaculum aerophilum str. IM2Q8ZXT682.8%Diamond
Sulfurisphaera tokodaii str. 7Q970Z669.2%Diamond
Methanocaldococcus jannaschii DSM 2661Q5805066.0%Diamond
Methanothrix thermoacetophila PTA0B7B761.5%Diamond
Saccharomyces cerevisiae S288CP2663754.3%Diamond
Schizosaccharomyces pombe 972h-Q1049054.3%Diamond
Neurospora crassa OR74AP1085753.3%Diamond
Archaeoglobus fulgidus DSM 4304O3025053.0%Diamond
Vairimorpha ceranae BRL01C4V8L152.7%Diamond
Encephalitozoon cuniculi GB-M1Q8SRS852.7%Diamond
Dictyostelium discoideumQ54N8351.2%Diamond
Methanothermobacter thermautotrophicus str. Delta HO2755249.6%Diamond
Methanopyrus kandleri AV19Q8TVM449.6%Diamond
Ignicoccus hospitalis KIN4/IA8A8T249.4%Diamond
Arabidopsis thalianaF4I11648.5%Diamond
Enterocytozoon bieneusi H348B7XHP644.2%Diamond
Aeropyrum pernix K1Q9YD9743.9%Diamond
Staphylothermus marinus F1A3DKS141.2%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
RBM27-POU4F3protein-coding127814297
SH3RF2protein-coding153769
PLAC8L1protein-coding153770
RBM27protein-coding54439
POU4F3protein-coding5459
PRELID2protein-coding153768
GRXCR2protein-coding643226
TCERG1protein-coding10915

Protein

Protein identifiers

Leucine–tRNA ligase, cytoplasmic — Q9P2J5 (reviewed: Q9P2J5)

Alternative names: Leucyl-tRNA synthetase

All UniProt accessions (13): A0A6I8PIP7, A0A6I8PIT3, A0A6I8PIV1, A0A6I8PL42, A0A6I8PLB3, A0A6I8PLB8, A0A6I8PRP1, A0A6I8PRS0, A0A6I8PRU9, A0A6I8PS05, A0A6I8PTV8, B4DER1, Q9P2J5

UniProt curated annotations — full annotation on UniProt →

Function. Aminoacyl-tRNA synthetase that catalyzes the specific attachment of leucine to its cognate tRNA (tRNA(Leu)). It performs tRNA aminoacylation in a two-step reaction: Leu is initially activated by ATP to form a leucyl-adenylate (Leu-AMP) intermediate; then the leucyl moiety is transferred to the acceptor 3’ end of the tRNA to yield leucyl-tRNA. To improve the fidelity of catalytic reactions, it is also able to hydrolyze misactivated aminoacyl-adenylate intermediates (pre-transfer editing) and mischarged aminoacyl-tRNAs (post-transfer editing).

Subunit / interactions. Part of the aminoacyl-tRNA synthetase multienzyme complex, also known as multisynthetase complex (MSC), that is composed of the aminoacyl-tRNA ligases for Arg (RARS1), Asp (DARS1), Gln (QARS1), Ile (IARS1), Leu (LARS1), Lys (KARS1), Met (MARS1) the bifunctional ligase for Glu and Pro (EPRS1) and the auxiliary subunits AIMP1/p43, AIMP2/p38 and EEF1E1/p18.

Subcellular location. Cytoplasm.

Disease relevance. Infantile liver failure syndrome 1 (ILFS1) [MIM:615438] A life-threatening disorder of hepatic function that manifests with acute liver failure in the first few months of life. Clinical features include anemia, renal tubulopathy, developmental delay, seizures, failure to thrive, and liver steatosis and fibrosis. The disease is caused by variants affecting the gene represented in this entry.

Activity regulation. 5-fluoro-1,3-dihydro-1-hydroxy-1,2-benzoxaborole inhibits LARS1 by forming a covalent adduct with the 3’ adenosine of tRNA(Leu) at the editing site, thus locking the enzyme in an inactive conformation.

Domain organisation. The structure of cytoplasmic leucine-tRNA ligase includes four main functional domains: the Rossmann-fold aminoacylation domain, the editing domain known as connective peptide 1 (CP1), the anticodon binding domain for tRNA recognition, and the vertebrate C-terminal (VC) domain for tRNA binding.

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

Isoforms (3)

UniProt IDNamesCanonical?
Q9P2J5-11yes
Q9P2J5-22
Q9P2J5-33

RefSeq proteins (4): NP_001304893, NP_001304894, NP_057544, NP_064502* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR001412aa-tRNA-synth_I_CSConserved_site
IPR002300aa-tRNA-synth_IaDomain
IPR004493Leu-tRNA-synth_Ia_arc/eukFamily
IPR009008Val/Leu/Ile-tRNA-synth_editHomologous_superfamily
IPR009080tRNAsynth_Ia_anticodon-bdHomologous_superfamily
IPR013155M/V/L/I-tRNA-synth_anticd-bdDomain
IPR014729Rossmann-like_a/b/a_foldHomologous_superfamily
IPR054509LARS1_ULDDomain
IPR055416RBD_LARS1Domain

Pfam: PF00133, PF08264, PF22947, PF24810

Enzyme classification (BRENDA)

  • EC 6.1.1.4 — leucine-tRNA ligase (BRENDA: 40 organisms, 173 substrates, 199 inhibitors, 375 Km, 348 kcat entries)

Substrate kinetics (BRENDA)

40 substrates with measured Km, best-characterized 15. Km ranges are aggregated across organisms/conditions.

SubstrateKm (mM)Measurements
L-LEUCINE0.0011–0.991
TRNALEU0.0001–0.027381
ATP0.08–5.868
TRNAGAGLEU0.0001–0.005821
TRNALEU(UAA)0.0013–0.004410
L-ISOLEUCINE0.25–148
TRNALEUCUN0.0002–0.0257
TRNALEUUUR—7
TRNAUAALEU0.0015–0.00256
L-LEU0.008–0.055
ILE-TRNALEU0.002–0.00254
L-ISOLEUCYL-TRNALEU0.0092–0.01734
L-METHIONINE0.983–7.53
TRNALEU FROM AQUIFEX AEOLICUS0.0003–0.00143
TRNALEU FROM ESCHERICHIA COLI0.0008–0.00153

Catalyzed reactions (Rhea)

  • tRNA(Leu) + L-leucine + ATP = L-leucyl-tRNA(Leu) + AMP + diphosphate (RHEA:11688)
  • L-methionyl-tRNA(Leu) + H2O = tRNA(Leu) + L-methionine + H(+) (RHEA:77535)

UniProt features (147 total): helix 57, strand 43, mutagenesis site 15, turn 11, binding site 5, modified residue 4, sequence variant 3, sequence conflict 3, splice variant 2, short sequence motif 2, chain 1, region of interest 1

Structure

Experimental structures (PDB)

8 structures by resolution:

PDBTitleMethodResolution (Å)
6LPFThe crystal structure of human cytoplasmic LRSX-RAY DIFFRACTION2.49
6LR6The crystal structure of human cytoplasmic LRSX-RAY DIFFRACTION3.01
6KIDCrystal structure of human leucyl-tRNA synthetase, ATP-bound formX-RAY DIFFRACTION3.15
6KIECrystal structure of human leucyl-tRNA synthetase, Leu-AMS-bound formX-RAY DIFFRACTION3.15
9W01Cryo-EM structure of LARS1:IARS1 complexELECTRON MICROSCOPY3.16
2WFDStructure of the human cytosolic leucyl-tRNA synthetase editing domainX-RAY DIFFRACTION3.25
6KQYCrystal structure of human leucyl-tRNA synthetase, Leucine-bound formX-RAY DIFFRACTION3.3
6KR7Crystal structure of methylated human leucyl-tRNA synthetase, Leu-AMS-bound formX-RAY DIFFRACTION4

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9P2J5-F190.780.74

Human Protein Atlas

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

Protein evidence: Evidence at protein level

Subcellular location (HPA, imaging): cytosol; nuclear bodies

Antibody reliability (HPA): IH supported · IF approved

Functional residue map

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

Ligand- & substrate-binding residues (5)

PositionRole
52L-leucine
54L-leucine
594L-leucine
597L-leucine
719ATP

Post-translational modifications (4)

TypePositions
Phosphoserine720, 167
N6-acetyllysine970, 1047

Mutagenesis-validated functional residues (15)

PositionPhenotype
236–256loss of leucyl-trna ligase activity. decreased activity in post-transfer editing of trna(leu) mischarged with methionine.
242reduced leucyl-trna ligase activity.
245no effect on leucyl-trna ligase activity.
245reduced leucyl-trna ligase activity.
245loss of leucyl-trna ligase activity.
247reduced leucyl-trna ligase activity.
250reduced leucyl-trna ligase activity. decreased activity in pre-transfer editing and no effect on post-transfer editing of trna(leu) …
250no effect on leucyl-trna ligase activity.
250reduced leucyl-trna ligase activity.
250loss of leucyl-trna ligase activity.
514–534loss of leucyl-trna ligase activity. decreased activity in post-transfer editing of trna(leu) mischarged with methionine.
519reduced leucyl-trna ligase activity.
523reduced leucyl-trna ligase activity.
525reduced leucyl-trna ligase activity.
527reduced leucyl-trna ligase activity.

Function

Pathways and Gene Ontology

Reactome pathways

2 curated (TAS) of 10; 0 disease pathways. Curated-first; evidence = TAS (manually curated) vs IEA (electronic inference).

10 pathways:

IDPathwayEvidence
R-HSA-379716Cytosolic tRNA aminoacylationcurated
R-HSA-9856649Transcriptional and post-translational regulation of MITF-M expression and activitycurated
R-HSA-1266738Developmental Biology—
R-HSA-9730414MITF-M-regulated melanocyte development—
R-HSA-1430728Metabolism—
R-HSA-71291Metabolism of amino acids and derivatives—
R-HSA-392499Metabolism of proteins—
R-HSA-2408522Selenoamino acid metabolismelectronic
R-HSA-72766Translation—
R-HSA-379724tRNA Aminoacylation—

MSigDB gene sets: 268 (showing top): GOBP_RESPONSE_TO_NITROGEN_COMPOUND, RODRIGUES_THYROID_CARCINOMA_ANAPLASTIC_UP, GOBP_AMINO_ACID_ACTIVATION, GOBP_RESPONSE_TO_ACID_CHEMICAL, GOBP_TRNA_METABOLIC_PROCESS, GOBP_POSITIVE_REGULATION_OF_TOR_SIGNALING, MEF2_02, GOBP_CELLULAR_RESPONSE_TO_ACID_CHEMICAL, GOBP_CELLULAR_RESPONSE_TO_OXYGEN_CONTAINING_COMPOUND, AACWWCAANK_UNKNOWN, GOBP_TRANSLATION, WANG_LMO4_TARGETS_DN, GOBP_RESPONSE_TO_OXYGEN_CONTAINING_COMPOUND, GOBP_CELLULAR_RESPONSE_TO_NITROGEN_COMPOUND, GOBP_POSITIVE_REGULATION_OF_INTRACELLULAR_SIGNAL_TRANSDUCTION

GO Biological Process (10): tRNA aminoacylation for protein translation (GO:0006418), glutaminyl-tRNA aminoacylation (GO:0006425), leucyl-tRNA aminoacylation (GO:0006429), cellular response to amino acid starvation (GO:0034198), cellular response to amino acid stimulus (GO:0071230), cellular response to L-leucine (GO:0071233), positive regulation of TORC1 signaling (GO:1904263), cellular response to leucine starvation (GO:1990253), translation (GO:0006412), aminoacyl-tRNA metabolism involved in translational fidelity (GO:0106074)

GO Molecular Function (9): aminoacyl-tRNA deacylase activity (GO:0002161), glutamine-tRNA ligase activity (GO:0004819), leucine-tRNA ligase activity (GO:0004823), GTPase activator activity (GO:0005096), ATP binding (GO:0005524), nucleotide binding (GO:0000166), aminoacyl-tRNA ligase activity (GO:0004812), protein binding (GO:0005515), ligase activity (GO:0016874)

GO Cellular Component (6): cytoplasm (GO:0005737), lysosome (GO:0005764), endoplasmic reticulum (GO:0005783), cytosol (GO:0005829), endomembrane system (GO:0012505), aminoacyl-tRNA synthetase multienzyme complex (GO:0017101)

Reactome top-level categories

7 top-level categories:

CategoryPathways
Metabolism of amino acids and derivatives1
tRNA Aminoacylation1
MITF-M-regulated melanocyte development1
Translation1
Metabolism1
Metabolism of proteins1
Developmental Biology1

GO top-level categories

50 GO namespaces:

CategoryTerms
cellular anatomical structure3
tRNA aminoacylation for protein translation2
catalytic activity, acting on a tRNA2
aminoacyl-tRNA ligase activity2
cytoplasm2
translation1
tRNA aminoacylation1
cellular response to starvation1
response to amino acid starvation1
response to amino acid1
cellular response to acid chemical1
response to L-leucine1
cellular response to amino acid stimulus1
cellular response to nitrogen compound1
cellular response to oxygen-containing compound1
positive regulation of TOR signaling1
TORC1 signaling1
regulation of TORC1 signaling1
cellular response to amino acid starvation1
peptidyltransferase activity1
translational initiation1
translational elongation1
translational termination1
macromolecule biosynthetic process1
protein metabolic process1
protein biosynthetic process1
tRNA metabolic process1
regulation of translational fidelity1
carboxylic ester hydrolase activity1
aminoacyl-tRNA metabolism involved in translational fidelity1
deacylase activity1
GTPase activity1
enzyme activator activity1
GTPase regulator activity1
adenyl ribonucleotide binding1
purine ribonucleoside triphosphate binding1
anion binding1
nucleoside phosphate binding1
heterocyclic compound binding1
ligase activity, forming carbon-oxygen bonds1
binding1
catalytic activity1
intracellular anatomical structure1
lytic vacuole1
endomembrane system1
intracellular membrane-bounded organelle1
vacuole1
plasma membrane1
intracellular protein-containing complex1
catalytic complex1

Experimentally-supported GO annotations

GO terms backed by direct experimental evidence (ECO experimental codes) — 17 of 25 annotations. The rest are phylogenetic / computational / electronic (IEA).

17 experimentally-supported GO terms:

GO termNSEvidence
cellular response to L-leucineBPmutant phenotype
cellular response to amino acid starvationBPmutant phenotype
cellular response to amino acid stimulusBPmutant phenotype
cellular response to leucine starvationBPmutant phenotype
glutaminyl-tRNA aminoacylationBPdirect assay
leucyl-tRNA aminoacylationBPdirect assay
positive regulation of TORC1 signalingBPmutant phenotype
aminoacyl-tRNA synthetase multienzyme complexCCdirect assay
cytoplasmCCdirect assay
cytosolCCdirect assay
endomembrane systemCCdirect assay
endoplasmic reticulumCCdirect assay
lysosomeCCmutant phenotype
GTPase activator activityMFmutant phenotype
aminoacyl-tRNA deacylase activityMFdirect assay
glutamine-tRNA ligase activityMFdirect assay
leucine-tRNA ligase activityMFdirect assay

Protein interactions and networks

STRING

showing 15 of 2,395 interactions by confidence (×1000):

Protein AProtein BPartner UniProtScore
LARS1TARS3A2RTX5952
LARS1TARS2Q9BW92951
LARS1TARS1P26639950
LARS1IARS1P41252932
LARS1IARS2Q9NSE4905
LARS1RPS14P06366880
LARS1AARS1P49588871
LARS1MARS1P56192848
LARS1VARS2Q5ST30848
LARS1YARS2Q9Y2Z4841
LARS1YARS1P54577839
LARS1MARS2Q96GW9838
LARS1PARS2Q7L3T8837
LARS1QARS1P47897836
LARS1SARS1P49591833

IntAct

Human interaction partners of LARS1 in IntAct, one row per partner (best MIscore; records = supporting IntAct interaction records).

17 partners by confidence:

PartnerInteraction typeMIscoreRecords
RARS1physical association0.7603
RRAGDphysical association0.6006
RPTORassociation0.5101
MTORassociation0.4601
ATP5MEphysical association0.4001
RPS10physical association0.4001
VIMphysical association0.4001
YWHAZphysical association0.4001
TARS3association0.3502
TARSL2association0.3501
DISC1physical association0.0001
DSCAMphysical association0.0001
ERGphysical association0.0001
IKBKGphysical association0.0001
OFD1physical association0.0001
RELAphysical association0.0001
TANKphysical association0.0001

SIGNOR signaling

3 signaling interactions:

AEffectBMechanism
ATF4“up-regulates quantity by expression”LARS1“transcriptional regulation”
LARS1“form complex”“Multiaminoacyl-tRNA synthetase”binding
LRRK2“down-regulates activity”LARS1phosphorylation

Protein complexes (CORUM) (1)

Experimentally-characterized complexes this protein is a subunit of (★ = the complex contains a known drug target).

1 complexes by size:

ComplexSubunitsMembers
Multisynthetase complex11IARS1, KARS1, QARS1, EPRS1, LARS1, MARS1, RARS1, AIMP1, AIMP2, DARS1, EEF1E1

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 17 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

PathwayPartnersFoldFDR
Cellular responses to stimuli614.5×1e-04
Cellular responses to stress514.2×4e-04

Disease & clinical

Genetic variants

Variant evidence for LARS1: 605 ClinVar records (28 pathogenic / likely pathogenic). Per-variant detail is on Sugi Variant.

ClinVar

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

ClassificationCount (floor)
Pathogenic14
Likely pathogenic14
Uncertain significance208
Likely benign177
Benign124

Top pathogenic / likely-pathogenic (15)

Showing the 15 best-reviewed of 28 pathogenic / likely-pathogenic ClinVar records, ranked by ClinVar review status (expert panel → multiple submitters → single submitter), then by number of submitting labs.

Variant IDHGVSClassificationReviewSubmitters
1939971NM_020117.11(LARS1):c.727A>T (p.Lys243Ter)Pathogeniccriteria provided, multiple submitters, no conflicts2
2533694NM_020117.11(LARS1):c.1237C>T (p.Arg413Ter)Pathogeniccriteria provided, multiple submitters, no conflicts2
214578NM_020117.11(LARS1):c.137_141del (p.Tyr46fs)Pathogeniccriteria provided, single submitter1
214579NM_020117.11(LARS1):c.84_85del (p.Arg28fs)Pathogeniccriteria provided, single submitter1
1048520NM_020117.11(LARS1):c.2504A>G (p.Tyr835Cys)Pathogeniccriteria provided, single submitter1
2803844NM_020117.11(LARS1):c.11_12del (p.Arg4fs)Pathogeniccriteria provided, single submitter1
3117894NM_020117.11(LARS1):c.2500A>T (p.Lys834Ter)Pathogeniccriteria provided, single submitter1
3699253NM_020117.11(LARS1):c.2383dup (p.Arg795fs)Pathogeniccriteria provided, single submitter1
4688932NM_020117.11(LARS1):c.1812del (p.Phe603_Tyr604insTer)Pathogeniccriteria provided, single submitter1
4712611NM_020117.11(LARS1):c.900del (p.Phe300fs)Pathogeniccriteria provided, single submitter1
4734755NM_020117.11(LARS1):c.904C>T (p.Gln302Ter)Pathogeniccriteria provided, single submitter1
4736046NM_020117.11(LARS1):c.2342G>A (p.Trp781Ter)Pathogeniccriteria provided, single submitter1
4738075NM_020117.11(LARS1):c.1621A>T (p.Lys541Ter)Pathogeniccriteria provided, single submitter1
388496NM_020117.11(LARS1):c.1306G>A (p.Gly436Ser)Likely pathogeniccriteria provided, single submitter1
388497NM_020117.11(LARS1):c.3064G>C (p.Glu1022Gln)Likely pathogeniccriteria provided, single submitter1

Per-variant reference — Sugi Variant

Explore LARS1’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; 25 predictions of 2,244):

Position(s)EffectΔscoreSites
5:146114313acceptor_loss1.0000
5:146120369–146120370donor_loss1.00004
5:146120504–146120505acceptor_loss1.00006
5:146122536donor_gain1.0000
5:146123980–146123981donor_loss1.00005
5:146124087acceptor_loss1.0000
5:146124096acceptor_gain1.0000
5:146124099acceptor_gain1.0000
5:146124102–146124104acceptor_gain1.00002
5:146126433–146126434donor_loss1.00003

AlphaMissense

2,842 missense substitutions predicted likely pathogenic (of 7,803 scored), across 728 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
M71790.9800.999
M99090.8660.992
H25180.9970.999
D59680.9930.998
D67680.9930.999
D75280.9930.999
D25080.9920.998
H68180.9890.998
H6080.9880.999
D39980.9880.994
H6380.9860.997
D74880.9810.998
D25280.9790.997
N5680.9750.999
H9180.9750.997
H68980.9640.989
D20080.9600.983
D40580.9460.986
F18480.9360.988
D79480.9320.971

HPA cancer prognostics

RNA cancer specificity: Low cancer specificity

Human Protein Atlas survival analysis — favorable = higher expression predicts better survival.

4 prognostic cancer types:

CancerPrognosticp-value
Liver Hepatocellular Carcinoma (TCGA)unfavorable3.06e-05
Kidney Chromophobe (TCGA)unfavorable9.75e-05
Kidney Renal Clear Cell Carcinoma (TCGA)favorable0.000188
Lung Squamous Cell Carcinoma (TCGA)favorable0.000893

Disease associations

OMIM: gene MIM:151350 | disease phenotypes: MIM:615438, MIM:613070

GenCC curated gene-disease

1 curated gene-disease records:

DiseaseClassificationInheritanceRecords
infantile liver failure syndrome 1StrongAutosomal recessive3

Genomics England panels (PanelApp)

Clinical diagnostic gene panels including this gene (8 panels, 8 green/diagnostic-grade). Confidence: green = diagnostic, amber = moderate.

8 panels:

PanelRating
Early onset or syndromic epilepsygreen
Hypotonic infantgreen
Intellectual disabilitygreen
Leukodystrophy, childhood onsetgreen
Likely inborn error of metabolismgreen
Paediatric disordersgreen
Undiagnosed metabolic disordersgreen
Unexplained death in infancy and sudden unexplained death in childhoodgreen

Mondo (2): infantile liver failure syndrome 1 (MONDO:0024568), acute infantile liver failure due to synthesis defect of mtDNA-encoded proteins (MONDO:0013111)

Orphanet (2): Acute infantile liver failure-multisystemic involvement syndrome (Orphanet:370088), Acute infantile liver failure due to synthesis defect of mtDNA-encoded proteins (Orphanet:217371)

HPO phenotypes

21 phenotypes (HPO-id order):

HPOTerm
HP:0000007Autosomal recessive inheritance
HP:0000252Microcephaly
HP:0000293Full cheeks
HP:0000407Sensorineural hearing impairment
HP:0001250Seizure
HP:0001252Hypotonia
HP:0001263Global developmental delay
HP:0001290Generalized hypotonia
HP:0001397Hepatic steatosis
HP:0001508Failure to thrive
HP:0001903Anemia
HP:0001972Macrocytic anemia
HP:0002007Frontal bossing
HP:0002194Delayed gross motor development
HP:0002240Hepatomegaly
HP:0002910Elevated circulating hepatic transaminase concentration
HP:0003128Lactic acidosis
HP:0003256Abnormality of the coagulation cascade
HP:0006554Acute hepatic failure
HP:0010511Long toe
HP:0100807Long fingers

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL3258 (SINGLE PROTEIN)

PharmGKB: 1 entry (CPIC guideline: no)

Binding affinities (BindingDB)

10 measured of 17 human assays (46 total across all organisms); most potent 10 below. Values come from heterogeneous assays and are not directly comparable.

LigandMeasureValue
CHEMBL4558130IC5070 nM
CHEMBL4104169IC50337 nM
CHEMBL5653589KD1440 nM
CHEMBL3764310IC5018700 nM
CHEMBL4061292IC5026400 nM
CHEMBL3764493IC5027600 nM
CHEMBL4074495IC5044900 nM
CHEMBL3765025IC5045800 nM
CHEMBL3763921IC50116000 nM
CHEMBL2436531IC50116000 nM

ChEMBL bioactivities

28 potent at pChembl≥5 of 42 total, top 28 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChemblTypeValueUnitMolecule
8.80IC501.6nMCHEMBL340082
8.22IC506nMCHEMBL341331
7.80IC5016nMCHEMBL421500
7.65IC5022.34nMLEUSA
7.48IC5033nMCHEMBL4174152
7.16IC5070.04nMCHEMBL4558130
6.80IC50160nMCHEMBL4163450
6.66IC50220nMCHEMBL4171458
6.58Kd264.8nMCHEMBL5653589
6.58ED50264.8nMCHEMBL5653589
6.47IC50337.1nMCHEMBL4104169
6.31IC50490nMCHEMBL4172643
6.22IC50600nMCHEMBL340082
6.14IC50730nMCHEMBL332104
6.07IC50850nMCHEMBL4159778
6.00IC501000nMCHEMBL264002
5.96IC501100nMCHEMBL4160841
5.94IC501150nMCHEMBL341331
5.92IC501200nMCHEMBL4163140
5.88IC501310nMCHEMBL45426
5.81IC501550nMCHEMBL74395
5.70IC502000nMCHEMBL4167692
5.64IC502300nMCHEMBL74755
5.47IC503400nMCHEMBL4171058
5.41IC503900nMCHEMBL4161986
5.35IC504500nMCHEMBL4174897
5.33Kd4627nMCHEMBL3752910
5.33ED504627nMCHEMBL3752910

PubChem BioAssay actives

27 with measured affinity, of 177 total; 24 most potent distinct compounds. Largely complementary to BindingDB; screening values are coarse (µM, 4 dp), so sub-nM hits tie at the floor.

CompoundAssayTypeValueUnit
[(2R,3S,4R,5R)-3,4-dihydroxy-5-[4-(4-phenoxyphenyl)-1,3-thiazol-2-yl]oxolan-2-yl]methyl N-[(2S)-2-amino-4-methylpentanoyl]sulfamate101350: Compound tested for the inhibition of Escherichia coli Leucyl-tRNA synthetaseic500.0016uM
[(2R,3S,4R,5R)-3,4-dihydroxy-5-[4-(2-phenylethyl)-1,3-thiazol-2-yl]oxolan-2-yl]methyl N-[(2S)-2-amino-4-methylpentanoyl]sulfamate101350: Compound tested for the inhibition of Escherichia coli Leucyl-tRNA synthetaseic500.0020uM
[(2R,3S,4R,5R)-3,4-dihydroxy-5-[4-[2-(4-phenoxyphenyl)ethyl]-1,3-thiazol-2-yl]oxolan-2-yl]methyl N-[(2S)-2-amino-4-methylpentanoyl]sulfamate101350: Compound tested for the inhibition of Escherichia coli Leucyl-tRNA synthetaseic500.0060uM
(4aR,6S,7R,7aS)-7-[[2-[[(2S)-2-amino-4-methylpentanoyl]sulfamoyl]acetyl]amino]-4-carbamoyl-6-hydroxy-2-methyl-4a,5,6,7a-tetrahydro-1H-cyclopenta[c]pyridine-7-carboxylic acid101353: Compound was evaluated for its inhibitory activity against Leucyl-tRNA synthetase from staphylococcus aureus WCUH29ic500.0160uM
[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl N-[(2S)-2-amino-4-methylpentanoyl]sulfamate1686658: Inhibition of catalytic activity of LRS (unknown origin) by aminoleucylation assayic500.0223uM
(2S)-2-amino-N-[3-(2-amino-6-phenylpyrimidin-4-yl)phenyl]sulfonyl-4-methylpentanamide1350198: Inhibition of human LeuRS assessed as reduction in ATP consumptionic500.0330uM
[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl N-[(2S,3R)-2,3-dihydroxy-4-methylpentanoyl]sulfamate1686658: Inhibition of catalytic activity of LRS (unknown origin) by aminoleucylation assayic500.0700uM
(2S)-2-amino-N-[3-(2-amino-6-methylpyrimidin-4-yl)phenyl]sulfonyl-4-methylpentanamide1350198: Inhibition of human LeuRS assessed as reduction in ATP consumptionic500.1600uM
(2S)-2-amino-4-methyl-N-naphthalen-2-ylsulfonylpentanamide1350198: Inhibition of human LeuRS assessed as reduction in ATP consumptionic500.2200uM
4-methyl-3-[(2-methyl-6-pyridin-3-ylpyrazolo[3,4-d]pyrimidin-4-yl)amino]-N-[3-(trifluoromethyl)phenyl]benzamide2148639: Binding affinity to human LARS incubated for 45 mins by Kinobead based pull down assaykd0.2648uM
[(2R,3S,4R,5R)-5-(6-amino-2-iodopurin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl N-[(2S)-2-hydroxy-4-methylpentanoyl]sulfamate1686658: Inhibition of catalytic activity of LRS (unknown origin) by aminoleucylation assayic500.3371uM
(2S)-2-amino-N-[3-(2-amino-4-pyridinyl)phenyl]sulfonyl-4-methylpentanamide1350198: Inhibition of human LeuRS assessed as reduction in ATP consumptionic500.4900uM
(2S)-2-amino-N-[3-(6-amino-2-pyridinyl)phenyl]sulfonyl-4-methylpentanamide1350198: Inhibition of human LeuRS assessed as reduction in ATP consumptionic500.8500uM
[(2R,3S,4R,5R)-3,4-dihydroxy-5-(4-phenyl-1,3-thiazol-2-yl)oxolan-2-yl]methyl N-[(2S,3S)-2-amino-3-methylpentanoyl]sulfamate101350: Compound tested for the inhibition of Escherichia coli Leucyl-tRNA synthetaseic501.0000uM
(2S)-2-amino-N-(benzenesulfonyl)-4-methylpentanamide1350198: Inhibition of human LeuRS assessed as reduction in ATP consumptionic501.1000uM
(2S)-2-amino-4-methyl-N-(3-pyridin-4-ylphenyl)sulfonylpentanamide1350198: Inhibition of human LeuRS assessed as reduction in ATP consumptionic501.2000uM
1-[5-[4-(4-chlorophenyl)phenoxy]pentyl]-3-pyridin-4-ylimidazolidin-2-one255776: Inhibitory activity against Echovirus 9 using plaque reduction assayic501.3100uM
(4aR,6S,7R,7aS)-7-[[2-[[(2S,3S)-2-amino-3-methylpentanoyl]sulfamoyl]acetyl]amino]-4-carbamoyl-6-hydroxy-2-methyl-4a,5,6,7a-tetrahydro-1H-cyclopenta[c]pyridine-7-carboxylic acid101353: Compound was evaluated for its inhibitory activity against Leucyl-tRNA synthetase from staphylococcus aureus WCUH29ic501.5500uM
(2S)-2-amino-4-methyl-N-[3-(6-methylpyrimidin-4-yl)phenyl]sulfonylpentanamide1350198: Inhibition of human LeuRS assessed as reduction in ATP consumptionic502.0000uM
(4aR,6S,7R,7aS)-7-[[2-[[(2S)-2-amino-3-methylbutanoyl]sulfamoyl]acetyl]amino]-4-carbamoyl-6-hydroxy-2-methyl-4a,5,6,7a-tetrahydro-1H-cyclopenta[c]pyridine-7-carboxylic acid101353: Compound was evaluated for its inhibitory activity against Leucyl-tRNA synthetase from staphylococcus aureus WCUH29ic502.3000uM
(2S)-2-amino-4-methyl-N-(3-phenylphenyl)sulfonylpentanamide1350198: Inhibition of human LeuRS assessed as reduction in ATP consumptionic503.4000uM
(2S)-2-amino-N-[3-(2-aminopyrimidin-4-yl)phenyl]sulfonyl-4-methylpentanamide1350198: Inhibition of human LeuRS assessed as reduction in ATP consumptionic503.9000uM
(2S)-2-amino-N-[3-[[2-(4-bromo-2-chlorophenoxy)acetyl]carbamothioylamino]phenyl]sulfonyl-4-methylpentanamide1350210: Inhibition of human cytoplasmic LeuRS assessed as reduction in protein synthesis measured after 10 mins in presence of [3H]Leu by scintillation counting methodic504.5000uM
4-methyl-3-[(1-methyl-6-pyridin-3-ylpyrazolo[3,4-d]pyrimidin-4-yl)amino]-N-[3-(trifluoromethyl)phenyl]benzamide2148639: Binding affinity to human LARS incubated for 45 mins by Kinobead based pull down assaykd4.6274uM

CTD chemical–gene interactions

55 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects cotreatment, decreases expression, affects expression4
Cyclosporineincreases expression4
bisphenol Aaffects expression, decreases expression3
trichostatin Aaffects cotreatment, decreases expression2
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, decreases expression2
Tetrachlorodibenzodioxindecreases expression2
Tretinoindecreases expression2
Cadmium Chlorideincreases abundance, increases palmitoylation, increases expression, decreases reaction2
aristolochic acid Idecreases expression1
bisphenol Fincreases expression1
TAK-243increases sumoylation1
geldanamycinincreases expression1
chloroacetaldehydedecreases expression1
methylmercuric chloridedecreases expression1
pyrogallol 1,3-dimethyl etherincreases expression, affects cotreatment, affects localization, decreases expression1
arseniteaffects binding, decreases reaction1
2-bromopalmitatedecreases reaction, increases abundance, increases palmitoylation1
ochratoxin Adecreases expression1
perfluorooctane sulfonic acidincreases expression1
CGP 52608affects binding, increases reaction1
nutlin 3affects cotreatment, increases secretion1
torcetrapibincreases expression1
ICG 001increases expression1
bisphenol Bincreases expression1
2,2’,4,4’-tetrabromodiphenyl etherdecreases expression1
dorsomorphinaffects cotreatment, decreases expression1
LDN 193189affects cotreatment, decreases expression1
bisphenol AFincreases expression1
Resveratrolaffects cotreatment, increases expression1
Temozolomideincreases expression1

ChEMBL screening assays

35 unique, capped per target: 32 binding, 2 admet, 1 functional

Representative assays (with source publication via chembl_document):

Assay IDTypeDescriptionSource paper
CHEMBL3769291BindingInhibition of human leucyl-tRNA synthetase assessed as reduction of [14C]-L-leucine ligation to tRNA incubated for 5 mins by scintillation counting method in presence of ATPDiscovery of potent anti-tuberculosis agents targeting leucyl-tRNA synthetase. — *Bioorg Med Chem*
CHEMBL4020313ADMETInhibition of human N-terminal 6His-tagged cytoplasmic LeuRS expressed in Escherichia coli BL21(DE3) assessed as L-[14C]leucine incorporation in to Escherichia coli tRNA after 20 mins by liquid scintillation counting analysisDiscovery of a Potent and Specific M. tuberculosis Leucyl-tRNA Synthetase Inhibitor: (S)-3-(Aminomethyl)-4-chloro-7-(2-hydroxyethoxy)benzo[c][1,2]oxaborol-1(3H)-ol (GSK656). — *J Med Chem*
CHEMBL885012FunctionalInhibitory activity against Echovirus 9 using plaque reduction assaySynthesis and antipicornavirus activity of (R)- and (S)-1-[5-(4’-chlorobiphenyl-4-yloxy)-3-methylpentyl]-3-pyridin-4-yl-imidazolidin-2-one. — *Bioorg Med Chem Lett*

Clinical trials (associated diseases)

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

showing 60 of 98 trials:

NCTPhaseStatusTitle
NCT01655212Phase 3TERMINATEDCongenital Cytomegalovirus: Efficacy of Antiviral Treatment in a Randomized Controlled Trial
NCT02005822Phase 3COMPLETEDCongenital Cytomegalovirus: Efficacy of Antiviral Treatment
NCT03374514Phase 3UNKNOWNCochlear Electrical Impedance and the Effect of Topical Dexamethasone on Cochlear Implant Surgery
NCT02497690Phase 2COMPLETEDEffectiveness of Therapy Via Telemedicine Following Cochlear Implants
NCT03107871Phase 2TERMINATEDRandomized Controlled Trial of Valganciclovir for Cytomegalovirus Infected Hearing Impaired Infants
NCT04120116Phase 2COMPLETEDFX-322 in Adults With Stable Sensorineural Hearing Loss
NCT05061758Phase 2WITHDRAWNA Trial of LY3056480 in Patients With SNLH
NCT07364747Phase 2RECRUITINGProtective Effect of Acetylcysteine Against Cisplatinum-Induced Ototoxicity: A Randomized Controlled Trial
NCT02038972Phase 1COMPLETEDSafety of Autologous Stem Cell Infusion for Children With Acquired Hearing Loss
NCT02259595Phase 1COMPLETEDStudy to Determine the Safety, Tolerability, and Pharmacokinetic Profile of HPN-07 and HPN-07 Plus NAC
NCT05514470Not specifiedWITHDRAWNImpact of Mutations in Aminoacyl tRNA Synthetases on Protein Translation and Cellular Stress
NCT06566066Not specifiedRECRUITINGRegister for Patients With Thyroid Hormone Resistance.
NCT02693704Phase 2/3COMPLETEDEvaluation of a Binaural Spatialization Method for Hearing Aids
NCT02882477Phase 2/3UNKNOWNTreatment of Wolfram Syndrome Type 2 With the Chelator Deferiprone and Incretin Based Therapy
NCT01267994Phase 1/2COMPLETEDA Clinical Trial of Anakinra for Steroid-Resistant Autoimmune Inner Ear Disease
NCT01902914Phase 1/2UNKNOWNEffectiveness of P02 Digital Hearing Aids
NCT02616172Phase 1/2SUSPENDEDAutologous Bone Marrow Harvest and Transplant for Sensorineural Hearing Loss
NCT03616223Phase 1/2COMPLETEDFX-322 in Sensorineural Hearing Loss
NCT04129775Phase 1/2COMPLETEDOTO-413 in Subjects With Speech-in-Noise Hearing Impairment
NCT04462198Phase 1/2COMPLETEDPhase I/IIa Study Evaluating Safety and Efficacy of an Intratympanic Dose of PIPE-505 in Subjects With Hearing Loss
NCT07032038Phase 1/2NOT_YET_RECRUITINGFirst In Human Randomised Trial of Rincell-1 in Adults With a Cochlear Implant
NCT06025097Early Phase 1COMPLETEDIntra-Tympanic Steroid With PRP Combination in Sensorineural Hearing Loss and Tinnitus.
NCT06707389Early Phase 1NOT_YET_RECRUITINGAutologous Blood Monocyte Vesicles for the Treatment of Sudden Deafness
NCT07472023Early Phase 1ENROLLING_BY_INVITATIONRegenerative Medicine and Stem Cell-Based Interventions for Inner Ear Trauma, Tinnitus, and Sensorineural Hearing Loss
NCT00023036Not specifiedCOMPLETEDClinical and Genetic Analysis of Enlarged Vestibular Aqueducts
NCT00023049Not specifiedCOMPLETEDGenetic Analysis of Hereditary Disorders of Hearing and Balance
NCT00261768Not specifiedCOMPLETEDEfficacy of Digital Noise Reduction Strategies: A Hearing Aid Trial
NCT00589511Not specifiedCOMPLETEDNucleus Freedom Cochlear Implant System Pediatric Post-approval Study
NCT00678899Not specifiedCOMPLETEDEvaluation of the Nucleus Hybrid™ L24 Cochlear Implant System
NCT00787189Not specifiedCOMPLETEDStudy of Low Level Laser Therapy and Word Recognition in Hearing Impaired Individuals
NCT01184248Not specifiedCOMPLETEDThe Effect of Sound Stimulation on Pure-tone Hearing Threshold
NCT01434446Not specifiedCOMPLETEDThe Effect of Sound Stimulation on Hearing Ability
NCT01749592Not specifiedCOMPLETEDSingle-sided Deafness and Cochlear Implants
NCT01781039Not specifiedCOMPLETEDInvestigation of Anatomical Correlates of Speech Discrimination
NCT02082431Not specifiedCOMPLETEDDetermine the Incidence of Long QT Amongst a Large Cohort of Subjects Diagnosed With Unilateral or Bilateral Sensorineural Hearing Loss.
NCT02093806Not specifiedUNKNOWNClinical Applications of Round Window Imaging Anatomy in Cochlear Implant Surgery
NCT02252601Not specifiedUNKNOWNEvaluation of the High Frequency Digit Triplet Test in Cystic Fibrosis
NCT02584361Not specifiedUNKNOWNCochlear Implant and Vestibular Function.
NCT02638883Not specifiedCOMPLETEDImplantation of the Cochlear™ Nucleus® Hybrid S Round Window (S-RW) in Adults
NCT02689349Not specifiedCOMPLETEDEsteem New Subject Enrollment Post Approval Study
NCT02698787Not specifiedCOMPLETEDFundamental Asynchronous Stimulus Timing Sound Coding Study
NCT02798783Not specifiedCOMPLETEDEnlarged Vestibular Aqueduct Registry
NCT03212924Not specifiedCOMPLETEDListening Effort in Cochlear Implant Users
NCT03260374Not specifiedUNKNOWNObjective Measures in Cochlear Implant
NCT03288753Not specifiedCOMPLETEDComparison Between Neuro 1 and Neuro 2 Cochlear Implant Speech Processors
NCT03467399Not specifiedCOMPLETEDClinical Evaluation of a Cochlear Implant System
NCT03718975Not specifiedCOMPLETEDQuality Control of CE-Certified Phonak Hearing Aids - 2018_28
NCT03746613Not specifiedCOMPLETEDClinal Evaluation of Navigation Based Functional Ear Surgery Using Image Guided and Robotically Assisted Techniques
NCT03858647Not specifiedTERMINATEDElectrode Placement and Audiologic Outcomes With the Advanced Bionics HiFocus L23 Electrode
NCT03938753Not specifiedCOMPLETEDQuality Control of CE-Certified Phonak Hearing Aids - 2018_42
NCT03992989Not specifiedCOMPLETEDQuality Control of CE-Certified Phonak Hearing Aids - 2019_19
NCT04102215Not specifiedUNKNOWNThe Efficacy of a Minimally Invasive Direct Cochlear Access Via the HEARO Procedure
NCT04108598Not specifiedUNKNOWNThe SeaSHeL National Prospective Cohort Study
NCT04183361Not specifiedUNKNOWNABR Characteristics and Salivary Cortisone Concentration in Noise-exposed Workers
NCT04241679Not specifiedCOMPLETEDAuditory Nerve Test System During Vestibular Schwannoma Resection
NCT04331015Not specifiedCOMPLETEDArtificial Intelligence in Diagnosis of DFNA9
NCT04450290Not specifiedCOMPLETEDDexamethasone-Eluting Cochlear Implant Electrode
NCT04610450Not specifiedCOMPLETEDThe Performance of a Robot-assisted Minimally Invasive Direct Cochlear Access for Cochlear Implantation
NCT04733950Not specifiedRECRUITINGCochlear Implanted Listening Effort and Hearing Attention
NCT04741009Not specifiedCOMPLETEDPerimodiolar Implant Performance in Adults With Low-Frequency Residual Hearing

Predicted chemistry — Sugi Predict

The predicted patent-compound landscape for LARS1 across ~30M SureChEMBL compounds — explore on Sugi Predict.