mutated Ligand Binding Site gene DataBase





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Gene Summary

Ligand Binding Site Mutation Information

Protein Structure Related Information

Gene Expression and Gene-Gene Network

Phenotype Information

Pharmacological Information

Conservation Information for LBS

Gene summary for YARS2
Gene summary
Basic gene Info.Gene symbolYARS2
Gene nametyrosyl-tRNA synthetase 2, mitochondrial
CytomapUCSC genome browser: 12p11.21
Type of geneprotein-coding
Descriptiontyrosine tRNA ligase 2, mitochondrialtyrosine--tRNA ligase, mitochondrial
Modification date20141207
dbXrefs MIM : 610957
Ensembl : ENSG00000139131
HPRD : 13025
Vega : OTTHUMG00000169454
ProteinUniProt: Q9Y2Z4
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_YARS2
BioGPS: 51067
PathwayNCI Pathway Interaction Database: YARS2
Pathway Commons: YARS2
ContextiHOP: YARS2
ligand binding site mutation search in PubMed: YARS2
UCL Cancer Institute: YARS2
Assigned class in mutLBSgeneDBC: This gene just belongs to mutLBSgenes.

Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez
GO:0043039tRNA aminoacylation15779907

Ligand binding site mutations for YARS2

Cancer type specific mutLBS sorted by frequency
LBSAAchange of nsSNVCancer type# samples
cf) Cancer type abbreviation. BLCA: Bladder urothelial carcinoma, BRCA: Breast invasive carcinoma, CESC: Cervical squamous cell carcinoma and endocervical adenocarcinoma, COAD: Colon adenocarcinoma, GBM: Glioblastoma multiforme, LGG: Brain lower grade glioma, HNSC: Head and neck squamous cell carcinoma, KICH: Kidney chromophobe, KIRC: Kidney renal clear cell carcinoma, KIRP: Kidney renal papillary cell carcinoma, LAML: Acute myeloid leukemia, LUAD: Lung adenocarcinoma, LUSC: Lung squamous cell carcinoma, OV: Ovarian serous cystadenocarcinoma, PAAD: Pancreatic adenocarcinoma, PRAD: Prostate adenocarcinoma, SKCM: Skin cutaneous melanoma, STAD: Stomach adenocarcinoma, THCA: Thyroid carcinoma, UCEC: Uterine corpus endometrial carcinoma.

Protein structure related information for YARS2
Relative protein structure stability change (ΔΔE) using Mupro 1.1
Mupro score denotes assessment of the effect of mutations on thermodynamic stability.
  (ΔΔE<0: mutation decreases stability, ΔΔE>0: mutation increases stability)
: nsSNV at non-LBS: nsSNV at LBS

nsSNVs sorted by the relative stability change of protein structure by each mutation
Blue: mutations of positive stability change. and red : the most recurrent mutation for this gene.
LBSAAchange of nsSNVRelative stability change
(MuPro1.1: Jianlin Cheng et al., Prediction of Protein Stability Changes for Single-Site Mutations Using Support Vector Machines, PROTEINS: Structure, Function, and Bioinformatics. 2006, 62:1125-1132)

Structure image for YARS2 from PDB

Differential gene expression and gene-gene network for YARS2
Differential gene expression between mutated and non-mutated LBS samples in all 16 major cancer types

Differential co-expressed gene network based on protein-protein interaction data (CePIN)
* Left PPI network was created from samples with mutations in the LBS of YARS2 and the right PPI network was created from samples without mutations in the LBS of YARS2. Only genes with p-value < 0.05 are shown.
Red circle: input gene. Orange circle: LBSgene. Blue circle: other gene.


Phenotype information for YARS2
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type
umls:C1838103Myopathy with lactic acidosis and sideroblastic anemia4Biomarker, GeneticVariation

Mutation level pathogenic information (ClinVar annotation)
Allele IDAA changeClinical significanceOriginPhenotype IDs

Pharmacological information for YARS2
Gene expression profile of anticancer drug treated cell-lines (CCLE)
Heatmap showing the correlation between gene expression and drug response across all the cell-lines. We chose the top 20 among 138 drugs.We used Pearson's correlation coefficient.

Gene-centered drug-gene interaction network
Drug information targeting mutLBSgene (Approved drugs only)
Drug statusDrugBank IDNameTypeDrug structure
Approved|nutraceuticalDB00135L-TyrosineSmall molecule

Gene-centered ligand-gene interaction network

Ligands binding to mutated ligand binding site of YARS2 go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS
TYAADENYLYL-TYROSINE3zxiBY77 D81 N173 Q225 G244 D246

Conservation information for LBS of YARS2
Multiple alignments for Q9Y2Z4 in multiple species
LBSAA sequence# speciesSpecies
A94VGHLLTLLGLF2Mus musculus, Rattus norvegicus
A94VGHLLALLGLF1Homo sapiens
A94LGNLVPLMVLL1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
A94VGNLVALMPLV1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
A94VGHLLPLMPLF1Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)
A94LGNLLGIIVLS1Arabidopsis thaliana
A94VGNLLVIMGLI1Drosophila melanogaster
D121TALLGDPSGRT2Mus musculus, Rattus norvegicus
D121TARLGDPSGRT1Homo sapiens
D121TGKVGDPSGRK1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
D121TAQLGDPSGRS1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
D121TAKIGDPTGRL1Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)
D121TGRVGDPSGKS1Arabidopsis thaliana
D121TGLIGDPSGRK1Drosophila melanogaster
D228VLQAYDFYYLF3Homo sapiens, Mus musculus, Rattus norvegicus
D228VLQAYDFYHLY1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
D228LLQAYDYSYLY1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
D228IMQGWDWFELF1Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)
D228LLQAYDFLHLF1Arabidopsis thaliana
D228IFQAYDWLHLL1Drosophila melanogaster
D246QLGGSDQLGNI3Homo sapiens, Mus musculus, Rattus norvegicus
D246QIGGSDQWGNI2Schizosaccharomyces pombe (strain 972 / ATCC 24843), Arabidopsis thaliana
D246QVGGNDQWGNI1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
D246QIGGSDQYGNI1Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)
D246QMGGSDQTGNL1Drosophila melanogaster
D81VYCGFDPTGDS2Mus musculus, Rattus norvegicus
D81IYCGFDPTADS1Homo sapiens
D81LYCGVDPTAQS1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
D81VYLGADPTAAS1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
D81AYVGIDPTAPS1Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)
D81VYCGFDPTAES1Arabidopsis thaliana
D81IYAGFDPTADS1Drosophila melanogaster
F80TVYCGFDPTGD2Mus musculus, Rattus norvegicus
F80TIYCGFDPTAD1Homo sapiens
F80KLYCGVDPTAQ1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
F80SVYLGADPTAA1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
F80GAYVGIDPTAP1Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)
F80RVYCGFDPTAE1Arabidopsis thaliana
F80SIYAGFDPTAD1Drosophila melanogaster
G243CRVQLGGSDQL3Homo sapiens, Mus musculus, Rattus norvegicus
G243VTIQVGGNDQW1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
G243VNLQIGGSDQW1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
G243VQMQIGGSDQY1Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)
G243INVQIGGSDQW1Arabidopsis thaliana
G243CCFQMGGSDQT1Drosophila melanogaster
G244RVQLGGSDQLG3Homo sapiens, Mus musculus, Rattus norvegicus
G244TIQVGGNDQWG1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
G244NLQIGGSDQWG1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
G244QMQIGGSDQYG1Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)
G244NVQIGGSDQWG1Arabidopsis thaliana
G244CFQMGGSDQTG1Drosophila melanogaster
G79QTVYCGFDPTG2Mus musculus, Rattus norvegicus
G79QTIYCGFDPTA1Homo sapiens
G79IKLYCGVDPTA1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
G79NSVYLGADPTA1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
G79IGAYVGIDPTA1Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)
G79LRVYCGFDPTA1Arabidopsis thaliana
G79QSIYAGFDPTA1Drosophila melanogaster
G90DSLHVGHLLTL2Mus musculus, Rattus norvegicus
G90DSLHVGHLLAL1Homo sapiens
G90QSLHLGNLVPL1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
G90ASLHVGNLVAL1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
G90PSLHVGHLLPL1Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)
G90ESLHLGNLLGI1Arabidopsis thaliana
G90DSLHVGNLLVI1Drosophila melanogaster
H88TGDSLHVGHLL2Mus musculus, Rattus norvegicus
H88TADSLHVGHLL1Homo sapiens
H88TAQSLHLGNLV1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
H88TAASLHVGNLV1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
H88TAPSLHVGHLL1Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)
H88TAESLHLGNLL1Arabidopsis thaliana
H88TADSLHVGNLL1Drosophila melanogaster
H91SLHVGHLLTLL2Mus musculus, Rattus norvegicus
H91SLHVGHLLALL1Homo sapiens
H91SLHLGNLVPLM1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
H91SLHVGNLVALM1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
H91SLHVGHLLPLM1Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)
H91SLHLGNLLGII1Arabidopsis thaliana
H91SLHVGNLLVIM1Drosophila melanogaster
L111HNVIALVGGST2Mus musculus, Rattus norvegicus
L111HNVIALVGGAT1Homo sapiens
L111HDIVTVIGGAT1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
L111FPVFTVIGDAT1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
L111YKAFTLIGGST1Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)
L111HQAVGLIGGAT1Arabidopsis thaliana
L111HRPIALVGGAT1Drosophila melanogaster
N173T-VLDNAAWFQ2Mus musculus, Rattus norvegicus
N173T-VLDNSAWYQ1Homo sapiens
N173T-PRNNFNWWK1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
N173WSIVRNSSWYE1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
N173RGIVNNNHWWN1Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)
N173V-IFNNYDWWK1Arabidopsis thaliana
N173I-IVNNADWYA1Drosophila melanogaster
Q225FYQVLQAYDFY3Homo sapiens, Mus musculus, Rattus norvegicus
Q225TYQVLQAYDFY1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Q225TYQLLQAYDYS1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
Q225TYPIMQGWDWF1Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)
Q225TYQLLQAYDFL1Arabidopsis thaliana
Q225TYQIFQAYDWL1Drosophila melanogaster
Q241YGCRVQLGGSD3Homo sapiens, Mus musculus, Rattus norvegicus
Q241ENVTIQVGGND1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Q241HSVNLQIGGSD1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
Q241QGVQMQIGGSD1Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)
Q241EGINVQIGGSD1Arabidopsis thaliana
Q241HNCCFQMGGSD1Drosophila melanogaster
Q247LGGSDQLGNIM3Homo sapiens, Mus musculus, Rattus norvegicus
Q247IGGSDQWGNIT2Schizosaccharomyces pombe (strain 972 / ATCC 24843), Arabidopsis thaliana
Q247VGGNDQWGNIT1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Q247IGGSDQYGNII1Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)
Q247MGGSDQTGNLM1Drosophila melanogaster
T116LVGGSTALLGD2Mus musculus, Rattus norvegicus
T116LVGGATARLGD1Homo sapiens
T116VIGGATGKVGD1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
T116VIGDATAQLGD1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
T116LIGGSTAKIGD1Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)
T116LIGGATGRVGD1Arabidopsis thaliana
T116LVGGATGLIGD1Drosophila melanogaster
Y221LAEFFYQVLQA3Homo sapiens, Mus musculus, Rattus norvegicus
Y221FNEFTYQVLQA1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Y221FAELTYQLLQA1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
Y221FAEFTYPIMQG1Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)
Y221YTEFTYQLLQA1Arabidopsis thaliana
Y221FTEFTYQIFQA1Drosophila melanogaster
Y77SPQTVYCGFDP2Mus musculus, Rattus norvegicus
Y77FPQTIYCGFDP1Homo sapiens
Y77DKIKLYCGVDP1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Y77NVNSVYLGADP1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
Y77--IGAYVGIDP1Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)
Y77APLRVYCGFDP1Arabidopsis thaliana
Y77--QSIYAGFDP1Drosophila melanogaster

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