mutLBSgeneDB

mutLBSgeneDB
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 symbol	YARS2
	Gene name	tyrosyl-tRNA synthetase 2, mitochondrial
	Synonyms	MLASA2\|MT-TYRRS\|TYRRS
	Cytomap	UCSC genome browser: 12p11.21
	Type of gene	protein-coding
	RefGenes	NM_001040436.2, NM_015936.1,
	Description	tyrosine tRNA ligase 2, mitochondrialtyrosine--tRNA ligase, mitochondrial
	Modification date	20141207
dbXrefs	MIM : 610957
	HGNC : HGNC
	Ensembl : ENSG00000139131
	HPRD : 13025
	Vega : OTTHUMG00000169454
Protein	UniProt: Q9Y2Z4 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_YARS2
	BioGPS: 51067
Pathway	NCI Pathway Interaction Database: YARS2
	KEGG: YARS2
	REACTOME: YARS2
	Pathway Commons: YARS2
Context	iHOP: YARS2
	ligand binding site mutation search in PubMed: YARS2
	UCL Cancer Institute: YARS2
Assigned class in mutLBSgeneDB	C: This gene just belongs to mutLBSgenes.

Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez

GO ID	GO Term	PubMed ID
GO:0043039	tRNA aminoacylation	15779907

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Ligand binding site mutations for YARS2

Cancer type specific mutLBS sorted by frequency

LBS	AAchange of nsSNV	Cancer type	# samples
Y77	T75S	GBM	1
N173	A175S	HNSC	1
D81	P82H	LUAD	1
G244,D246	S245C	OV	1
Q225	A226T	STAD	1

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.

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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.

LBS	AAchange of nsSNV	Relative stability change
Q225	A226T	-1.2223103
D81	P82H	-1.1429145
Y77	T75S	-0.97562833
N173	A175S	-0.77268866
G244	S245C	-0.3690209
D246	S245C	-0.3690209

(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

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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.

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Phenotype information for YARS2

Gene level disease information (DisGeNet)

Disease ID	Disease name	# PubMed	Association type
umls:C1838103	Myopathy with lactic acidosis and sideroblastic anemia	4	Biomarker, GeneticVariation
umls:C3150802	MYOPATHY, LACTIC ACIDOSIS, AND SIDEROBLASTIC ANEMIA 2	2	GeneticVariation

Mutation level pathogenic information (ClinVar annotation)

Allele ID

AA change

Clinical significance

Origin

Phenotype IDs

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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 status	DrugBank ID	Name	Type	Drug structure
Approved\|nutraceutical	DB00135	L-Tyrosine	Small molecule

Gene-centered ligand-gene interaction network

Ligands binding to mutated ligand binding site of YARS2 go to BioLip

Ligand ID	Ligand short name	Ligand long name	PDB ID	PDB name	mutLBS
TYA		ADENYLYL-TYROSINE	3zxi	A	D81 N173 Q225 G244 D246
TYA		ADENYLYL-TYROSINE	3zxi	B	Y77 D81 N173 Q225 G244 D246
YSA		TYROSYLADENYLATE	2pid	A	Y77 D81 Q225 G244 D246
YSA		TYROSYLADENYLATE	2pid	B	Y77 D81 Q225 G244 D246

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Conservation information for LBS of YARS2

Multiple alignments for Q9Y2Z4 in multiple species

LBS	AA sequence	# species	Species
A94	VGHLLTLLGLF	2	Mus musculus, Rattus norvegicus
A94	VGHLLALLGLF	1	Homo sapiens
A94	LGNLVPLMVLL	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
A94	VGNLVALMPLV	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
A94	VGHLLPLMPLF	1	Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)
A94	LGNLLGIIVLS	1	Arabidopsis thaliana
A94	VGNLLVIMGLI	1	Drosophila melanogaster
D121	TALLGDPSGRT	2	Mus musculus, Rattus norvegicus
D121	TARLGDPSGRT	1	Homo sapiens
D121	TGKVGDPSGRK	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
D121	TAQLGDPSGRS	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
D121	TAKIGDPTGRL	1	Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)
D121	TGRVGDPSGKS	1	Arabidopsis thaliana
D121	TGLIGDPSGRK	1	Drosophila melanogaster
D228	VLQAYDFYYLF	3	Homo sapiens, Mus musculus, Rattus norvegicus
D228	VLQAYDFYHLY	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
D228	LLQAYDYSYLY	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
D228	IMQGWDWFELF	1	Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)
D228	LLQAYDFLHLF	1	Arabidopsis thaliana
D228	IFQAYDWLHLL	1	Drosophila melanogaster
D246	QLGGSDQLGNI	3	Homo sapiens, Mus musculus, Rattus norvegicus
D246	QIGGSDQWGNI	2	Schizosaccharomyces pombe (strain 972 / ATCC 24843), Arabidopsis thaliana
D246	QVGGNDQWGNI	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
D246	QIGGSDQYGNI	1	Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)
D246	QMGGSDQTGNL	1	Drosophila melanogaster
D81	VYCGFDPTGDS	2	Mus musculus, Rattus norvegicus
D81	IYCGFDPTADS	1	Homo sapiens
D81	LYCGVDPTAQS	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
D81	VYLGADPTAAS	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
D81	AYVGIDPTAPS	1	Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)
D81	VYCGFDPTAES	1	Arabidopsis thaliana
D81	IYAGFDPTADS	1	Drosophila melanogaster
F80	TVYCGFDPTGD	2	Mus musculus, Rattus norvegicus
F80	TIYCGFDPTAD	1	Homo sapiens
F80	KLYCGVDPTAQ	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
F80	SVYLGADPTAA	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
F80	GAYVGIDPTAP	1	Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)
F80	RVYCGFDPTAE	1	Arabidopsis thaliana
F80	SIYAGFDPTAD	1	Drosophila melanogaster
G243	CRVQLGGSDQL	3	Homo sapiens, Mus musculus, Rattus norvegicus
G243	VTIQVGGNDQW	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
G243	VNLQIGGSDQW	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
G243	VQMQIGGSDQY	1	Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)
G243	INVQIGGSDQW	1	Arabidopsis thaliana
G243	CCFQMGGSDQT	1	Drosophila melanogaster
G244	RVQLGGSDQLG	3	Homo sapiens, Mus musculus, Rattus norvegicus
G244	TIQVGGNDQWG	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
G244	NLQIGGSDQWG	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
G244	QMQIGGSDQYG	1	Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)
G244	NVQIGGSDQWG	1	Arabidopsis thaliana
G244	CFQMGGSDQTG	1	Drosophila melanogaster
G79	QTVYCGFDPTG	2	Mus musculus, Rattus norvegicus
G79	QTIYCGFDPTA	1	Homo sapiens
G79	IKLYCGVDPTA	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
G79	NSVYLGADPTA	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
G79	IGAYVGIDPTA	1	Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)
G79	LRVYCGFDPTA	1	Arabidopsis thaliana
G79	QSIYAGFDPTA	1	Drosophila melanogaster
G90	DSLHVGHLLTL	2	Mus musculus, Rattus norvegicus
G90	DSLHVGHLLAL	1	Homo sapiens
G90	QSLHLGNLVPL	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
G90	ASLHVGNLVAL	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
G90	PSLHVGHLLPL	1	Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)
G90	ESLHLGNLLGI	1	Arabidopsis thaliana
G90	DSLHVGNLLVI	1	Drosophila melanogaster
H88	TGDSLHVGHLL	2	Mus musculus, Rattus norvegicus
H88	TADSLHVGHLL	1	Homo sapiens
H88	TAQSLHLGNLV	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
H88	TAASLHVGNLV	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
H88	TAPSLHVGHLL	1	Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)
H88	TAESLHLGNLL	1	Arabidopsis thaliana
H88	TADSLHVGNLL	1	Drosophila melanogaster
H91	SLHVGHLLTLL	2	Mus musculus, Rattus norvegicus
H91	SLHVGHLLALL	1	Homo sapiens
H91	SLHLGNLVPLM	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
H91	SLHVGNLVALM	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
H91	SLHVGHLLPLM	1	Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)
H91	SLHLGNLLGII	1	Arabidopsis thaliana
H91	SLHVGNLLVIM	1	Drosophila melanogaster
L111	HNVIALVGGST	2	Mus musculus, Rattus norvegicus
L111	HNVIALVGGAT	1	Homo sapiens
L111	HDIVTVIGGAT	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
L111	FPVFTVIGDAT	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
L111	YKAFTLIGGST	1	Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)
L111	HQAVGLIGGAT	1	Arabidopsis thaliana
L111	HRPIALVGGAT	1	Drosophila melanogaster
N173	T-VLDNAAWFQ	2	Mus musculus, Rattus norvegicus
N173	T-VLDNSAWYQ	1	Homo sapiens
N173	T-PRNNFNWWK	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
N173	WSIVRNSSWYE	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
N173	RGIVNNNHWWN	1	Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)
N173	V-IFNNYDWWK	1	Arabidopsis thaliana
N173	I-IVNNADWYA	1	Drosophila melanogaster
Q225	FYQVLQAYDFY	3	Homo sapiens, Mus musculus, Rattus norvegicus
Q225	TYQVLQAYDFY	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Q225	TYQLLQAYDYS	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
Q225	TYPIMQGWDWF	1	Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)
Q225	TYQLLQAYDFL	1	Arabidopsis thaliana
Q225	TYQIFQAYDWL	1	Drosophila melanogaster
Q241	YGCRVQLGGSD	3	Homo sapiens, Mus musculus, Rattus norvegicus
Q241	ENVTIQVGGND	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Q241	HSVNLQIGGSD	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
Q241	QGVQMQIGGSD	1	Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)
Q241	EGINVQIGGSD	1	Arabidopsis thaliana
Q241	HNCCFQMGGSD	1	Drosophila melanogaster
Q247	LGGSDQLGNIM	3	Homo sapiens, Mus musculus, Rattus norvegicus
Q247	IGGSDQWGNIT	2	Schizosaccharomyces pombe (strain 972 / ATCC 24843), Arabidopsis thaliana
Q247	VGGNDQWGNIT	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Q247	IGGSDQYGNII	1	Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)
Q247	MGGSDQTGNLM	1	Drosophila melanogaster
T116	LVGGSTALLGD	2	Mus musculus, Rattus norvegicus
T116	LVGGATARLGD	1	Homo sapiens
T116	VIGGATGKVGD	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
T116	VIGDATAQLGD	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
T116	LIGGSTAKIGD	1	Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)
T116	LIGGATGRVGD	1	Arabidopsis thaliana
T116	LVGGATGLIGD	1	Drosophila melanogaster
Y221	LAEFFYQVLQA	3	Homo sapiens, Mus musculus, Rattus norvegicus
Y221	FNEFTYQVLQA	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Y221	FAELTYQLLQA	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
Y221	FAEFTYPIMQG	1	Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)
Y221	YTEFTYQLLQA	1	Arabidopsis thaliana
Y221	FTEFTYQIFQA	1	Drosophila melanogaster
Y77	SPQTVYCGFDP	2	Mus musculus, Rattus norvegicus
Y77	FPQTIYCGFDP	1	Homo sapiens
Y77	DKIKLYCGVDP	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Y77	NVNSVYLGADP	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
Y77	--IGAYVGIDP	1	Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)
Y77	APLRVYCGFDP	1	Arabidopsis thaliana
Y77	--QSIYAGFDP	1	Drosophila melanogaster