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	Gene Summary
	Translation studies in PubMed
	Exon Skipping Events
	Expression
	Expression Regulation
	Associated Genes
	Protein 3D Structure
	Protein-Protein Interaction
	Mutations
	Prognostic Analysis
	Gender Association
	Age Association
	Related Drugs
	Related Diseases

Translation Factor: YARS2 (NCBI Gene ID:51067)

Gene Summary

Gene Summary

Gene Information	Gene Name: YARS2
	Gene ID: 51067
	Gene Symbol	YARS2
	Gene ID	51067
	Gene Name	tyrosyl-tRNA synthetase 2
	Synonyms	CGI-04\|MLASA2\|MT-TYRRS\|TYRRS
	Cytomap	12p11.21
	Type of Gene	protein-coding
	Description	tyrosine--tRNA ligase, mitochondrialtyrosine tRNA ligase 2, mitochondrialtyrosyl-tRNA synthetase 2, mitochondrial
	Modification date	20200313
	UniProtAcc	Q9Y2Z4

Child GO biological process term(s) under GO:0006412

GO ID	GO term
GO:0032543	Mitochondrial translation
GO:0006418	tRNA aminoacylation for protein translation
GO:0006412	Translation

Gene ontology of translaction factor with evidence of Inferred from Direct Assay (IDA) from Entrez

Partner	Gene	GO ID	GO term	PubMed ID
Hgene	YARS2	GO:0043039	tRNA aminoacylation	15779907\|15840810\|17997975

Inferred gene age of translation factor.

Gene	Inferred gene age group among (0 - 67.6], (67.6 - 355.7], (355.7 - 733], (733 - 1119.25], >1119.25
YARS2	>1119.25

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Translation Studies in PubMed

We searched PubMed using 'YARS2[title] AND translation [title] AND human.'

Gene	Title	PMID
YARS2	.	.

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Exon Skipping Events

Skipped exons in TCGA and GTEx based on Ensembl gene isoform structure.
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
For more annotations, please visit our ExonSkipDB.

Open reading frame (ORF) analsis of exon skipping events based on Ensembl gene isoform structure.
* Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser.

ENST	Exon skip start (DNA)	Exon Skip end (DNA)	ORF
ENST00000324868	32902870	32903041	In-frame
ENST00000324868	32906851	32907019	In-frame

Exon skipping position in the amino acid sequence.

ENST	Exon skip start (DNA)	Exon Skip end (DNA)	Len(transcript seq)	Exon skip start (mRNA)	Exon Skip end (mRNA)	Len(amino acid seq)	Exon skip start (AA)	Exon Skip end (AA)
ENST00000324868	32902870	32903041	2139	1132	1302	477	368	424
ENST00000324868	32906851	32907019	2139	808	975	477	260	315

Potentially (partially) lost protein functional features of UniProt.

UniProtAcc	Exon skip start (AA)	Exon Skip end (AA)	Function feature start (AA)	Function feature end (AA)	Functional feature type	Functional feature desc.
Q9Y2Z4	368	424	17	477	Chain	ID=PRO_0000035830;Note=Tyrosine--tRNA ligase%2C mitochondrial
Q9Y2Z4	260	315	17	477	Chain	ID=PRO_0000035830;Note=Tyrosine--tRNA ligase%2C mitochondrial
Q9Y2Z4	260	315	281	285	Motif	Note="KMSKS" region;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q9Y2Z4	260	315	274	274	Binding site	Note=ATP%3B via amide nitrogen and carbonyl oxygen;Ontology_term=ECO:0000244,ECO:0000244,ECO:0000269;evidence=ECO:0000244\|PDB:2PID,ECO:0000244\|PDB:3ZXI,ECO:0000269\|PubMed:17997975;Dbxref=PMID:17997975
Q9Y2Z4	260	315	284	284	Binding site	Note=ATP;Ontology_term=ECO:0000250;evidence=ECO:0000250
Q9Y2Z4	260	315	272	272	Sequence conflict	Note=P->T;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q9Y2Z4	260	315	311	311	Sequence conflict	Note=D->E;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q9Y2Z4	260	315	248	261	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2PID
Q9Y2Z4	260	315	267	271	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2PID
Q9Y2Z4	260	315	291	293	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2PID
Q9Y2Z4	260	315	294	296	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2PID
Q9Y2Z4	260	315	299	307	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2PID
Q9Y2Z4	260	315	311	321	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2PID
Q9Y2Z4	368	424	344	372	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2PID

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Expression

Gene expression level across TCGA pancancer

Gene expression level across GTEx pantissue

Expression level of gene isoforms across TCGA pancancer

Expression level of gene isoforms across GTEx pantissue

Cancer(tissue) type-specific expression level of Translation factor using z-score distriution

Differential expression between tumor and matched normal (in the cancer types with more than 10 matched samples)

Cancer type	Translation factor	FC	adj.pval
HNSC	YARS2	1.51758504797514	0.00498432417884942
ESCA	YARS2	-2.00710684466974	0.0185546875

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Expression Regulation

Translation factor expression regulation through miRNA binding

Cancer type

Gene

miRNA

TargetScan binding score (Context++ score percentile)

Coefficient

Pvalue

Translation factor expression regulation through methylation in the promoter of Translation factor

Cancer type	Gene	methyl group b	methyl group a	DEG pval	avg methyl in b	avg methyl in a	avg exp in b	avg exp in a
LIHC	YARS2	2	1	0.00702382390777724	0.204149404761905	0.172987821285141	-1.08771464132536	-0.64434651740069

Translation factor expression regulation through methylation in the gene body of Translation factor (positive regulation)

Cancer type

Gene

methyl group b

methyl group a

DEG pval

avg methyl in b

avg methyl in a

avg exp in b

avg exp in a

Translation factor expression regulation through copy number variation of Translation factor

Cancer type	Gene	Coefficient	Pvalue
LIHC	YARS2	0.112602307	0.009084593
SARC	YARS2	0.34080405	0.032333839
KIRP	YARS2	-0.047418563	0.048248176

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Associated Genes

Strongly correlated genes belong to cellular important gene groups with YARS2 (coefficient>0.8, pval<0.05, node color based on FC between tumor and matched normal). Significantly associated important genes in the individual cancer types. * Cell metabolism gene: cell metabolism genes from REACTOME (black edge), IUPHAR: drug target genes from IUPHAR (blue edge), Kinase: human kinase genes (brown edge), CGC: cancer gene census genes (orange edge), TSG: tumor suppresor genes (purple edge), Epifactor: epigenetic factors (light blue edge), TF: transcription factors (green)

Cancer type

Gene group

Translation factor

Correlated gene

Coefficient

Pvalue

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Protein structure

Protein 3D structure
Visit iCn3D.

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Protein-Protein Interaction

Protein-protein interaction networks
* Overlap between up-regulated DEGs (log2FC<-1 and adj.P<0.05) and STRING PPI network (center: Translation factor, node: DEGs, edges: weighted by -log2(adj.P))

Overlap between down-regulated DEGs (log2FC>1 and adj.P<0.05) and STRING PPI network (center: Translation factor, node: DEGs, edges: weighted by -log2(adj.P))

* Edge colors based on TCGA cancer types.

* Overlap between DEGs (log2FC>1 and adj.P<0.05) and STRING PPI network per cancer (center: Translation factor, node: DEGs, node color: log2FC, edges: weighted by -log2(adj.P))

Cancer type	Translation factor	Interacting protein coding gene	FC	adj.pval
STAD	YARS2	LARS2	-3.14243034518345	0.00019507110118866
STAD	YARS2	YARS	-6.49411565641968	0.000280400272458792
KIRP	YARS2	EARS2	2.04485161641576	0.000364991836249828
HNSC	YARS2	YARS	1.29642872422682	0.000481783007217019
THCA	YARS2	LARS2	1.46480152873302	0.000495104848866816
STAD	YARS2	AARS	-1.37044043826934	0.000657554250210524
STAD	YARS2	EPRS	-1.48171581324647	0.000789262883452143
LUSC	YARS2	RARS2	1.87851633718952	0.00105278618568408
KIRP	YARS2	RARS2	-1.62015129839089	0.00733334058895707
KICH	YARS2	TRUB2	-2.06154942711577	0.00882232189178467
HNSC	YARS2	GARS	1.31758956739856	0.0139046201916244
ESCA	YARS2	TRUB2	-1.63055491619549	0.0185546875
CHOL	YARS2	TRUB2	-2.3070167517537	0.02734375
BRCA	YARS2	LARS2	-5.48583270161281	1.12177735729832e-06
THCA	YARS2	YARS	-1.52851760350795	1.38467683131598e-09
LUAD	YARS2	SARS2	-1.6825303693262	1.52668366875458e-07
BRCA	YARS2	TRUB2	-2.53279756068983	1.7326162077773e-13
LUSC	YARS2	TRUB2	-3.50473378801546	1.91629083762368e-08
LIHC	YARS2	EPRS	-7.10731017811505	2.28054594243154e-08
LUAD	YARS2	LARS2	-1.17851720308655	2.81164525558733e-06
KICH	YARS2	YARS	-2.00632816869948	2.98023223876953e-07
LUSC	YARS2	EARS2	-4.79437223180067	3.23227619897643e-09
PRAD	YARS2	WARS2	2.22021907294155	3.33417295851411e-06
LUAD	YARS2	TRUB2	-1.92983802030623	3.47524877088934e-09
BRCA	YARS2	YARS	-2.58863291399932	3.63754942015711e-21
LUAD	YARS2	EARS2	-4.660053370012	3.79251210274868e-11
BLCA	YARS2	EARS2	-4.74352280775662	3.814697265625e-06
KICH	YARS2	LARS2	1.44112931619469	4.17232513427734e-06
STAD	YARS2	EARS2	-1.69983591205674	4.39747236669064e-05
LUAD	YARS2	AARS	-6.1139400689607	4.40386642176516e-08
THCA	YARS2	GARS	-1.56246373012062	8.23769499323433e-10
KIRC	YARS2	SARS2	1.02423405449982	8.65930768143138e-05
PRAD	YARS2	EPRS	-1.76339127457265	9.52775218277559e-05

Protein-protein interactors with this translation factor (BIOGRID-3.4.160)

PPI interactors with YARS2

CDC20, USP49, ICT1, Ybx1, CUL3, CAND1, DDRGK1, FAM9B, BMI1, HNRNPDL, ZC3H3, MRPL4, HNRNPA1, TRUB2, MRPL39, RBMX, ADAM12, CAPN3, YARS, OFD1, CNTRL, FBF1, MRPL50, CISD3, ATOH1, LYRM2, TMEM184A, CIRBP, RBM3, ZNF324B, FASTKD2, ATP5D, DDX28, MRPL12, RPUSD3, UQCC2, RBM42, APOBEC3D, UQCC1, KLHL2, HNRNPK, HSPD1, MRM1, NXF1, UBC, EFTUD2, RECQL4, PDK1, TRMT61B, SUCLG1, FH, ECHS1, OXCT1, SUCLA2, ETHE1, APEX1, SNRNP70, BIRC3, SYVN1, AGTRAP, PLEKHA4, MLLT1, HSCB, GRSF1, CIT, ANLN, KIF23, AUH, C21orf33, LRPPRC, MDH2, METTL17, APOO, MRRF, MTG2, MTIF2, SSBP1, TBRG4, TSFM, EXD2, C12orf49, AARS2, COX8A, CS, PDHA1, TRAP1, GADD45GIP1, SRSF3, RBMS2, FAM120A, IGF2BP3, ABHD10, HNRNPU, PTCD1, ISCA1, YBX2, MRPL30, RBM47, MRPL52, MRPL2, MSI1, UQCRFS1, PRR3, WBSCR16, HNRNPCL1, NUPL2, MALSU1, MAP7, PREPL, LARS2, FECH, CHDH, ACSF2, TARS2, AMACR, SPTB, METTL15, ACSF3, COQ9, SDR39U1, PCCB, PC, IARS2, GUF1, MRPL10, GATB, RPUSD4, ADCK4, POLG, MTPAP, IVD, PCCA, ACAD10, IDH3G, MRPS30, DARS2, CDK5RAP1, GFM2, CRAT, ABHD11, PCYOX1, GTPBP10, NARS2, PPOX, MTERF3, D2HGDH, MTHFD1L, GSTK1, SUPV3L1, VARS2, GTPBP6, MTFMT, PUS1, ATPAF2, MRPL51, PNPT1, RARS2, OGDHL, ATPAF1, PARS2, NR2F6, CPT2, CPS1, MIPEP, PVR, UBXN6, CYP24A1, FASTKD5, MUT, C14orf159, ALDH18A1, MRPS18A, CLPX, MCAT, FTSJ2, CECR5, SARDH, VWA8, FAHD1, GLS, POLRMT, NT5DC3, NSUN4, L2HGDH, AK4, GTPBP3, RBMS3, BCKDHA, KIAA0391, ACAA2, EARS2, ACSM5, TMLHE, GFM1, MRPL13, ZNF346, RSAD1, NGRN, MRPL16, ERAL1, QRSL1, ALDH4A1, BCKDK, MTO1, MCCC1, nsp1, nsp4,

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Mutations

Clinically associated variants from ClinVar.

Gene	Chr	Position	RefSeq	VarSeq	RefSeeq	VarType	Pathogenic	Disease	VarInfo
YARS2	chr12	32899511	T	A	single_nucleotide_variant	Uncertain_significance	Myopathy,_lactic_acidosis,_and_sideroblastic_anemia_2\|Hereditary_Sideroblastic_Anemia_with_Myopathy_and_Lactic_Acidosis	SO:0001624\|3_prime_UTR_variant	SO:0001624\|3_prime_UTR_variant
YARS2	chr12	32899543	C	T	single_nucleotide_variant	Uncertain_significance	Myopathy,_lactic_acidosis,_and_sideroblastic_anemia_2	SO:0001624\|3_prime_UTR_variant	SO:0001624\|3_prime_UTR_variant
YARS2	chr12	32899660	C	T	single_nucleotide_variant	Uncertain_significance	Myopathy,_lactic_acidosis,_and_sideroblastic_anemia_2	SO:0001624\|3_prime_UTR_variant	SO:0001624\|3_prime_UTR_variant
YARS2	chr12	32899669	G	A	single_nucleotide_variant	Likely_benign	Myopathy,_lactic_acidosis,_and_sideroblastic_anemia_2	SO:0001624\|3_prime_UTR_variant	SO:0001624\|3_prime_UTR_variant
YARS2	chr12	32899761	C	T	single_nucleotide_variant	Uncertain_significance	Myopathy,_lactic_acidosis,_and_sideroblastic_anemia_2	SO:0001624\|3_prime_UTR_variant	SO:0001624\|3_prime_UTR_variant
YARS2	chr12	32900114	T	C	single_nucleotide_variant	Uncertain_significance	Mitochondrial_myopathy_and_sideroblastic_anemia\|Myopathy,_lactic_acidosis,_and_sideroblastic_anemia_2	SO:0001624\|3_prime_UTR_variant	SO:0001624\|3_prime_UTR_variant
YARS2	chr12	32900145	T	C	single_nucleotide_variant	Uncertain_significance	Myopathy,_lactic_acidosis,_and_sideroblastic_anemia_2	SO:0001583\|missense_variant	SO:0001583\|missense_variant
YARS2	chr12	32900176	T	C	single_nucleotide_variant	Likely_pathogenic	not_provided	SO:0001583\|missense_variant	SO:0001583\|missense_variant
YARS2	chr12	32900210	AAT	TC	Indel	Likely_pathogenic	not_provided	SO:0001589\|frameshift_variant	SO:0001589\|frameshift_variant
YARS2	chr12	32900269	T	C	single_nucleotide_variant	Pathogenic	Myopathy,_lactic_acidosis,_and_sideroblastic_anemia_2	SO:0001583\|missense_variant	SO:0001583\|missense_variant
YARS2	chr12	32900298	C	CT	Duplication	Conflicting_interpretations_of_pathogenicity	not_provided	SO:0001574\|splice_acceptor_variant	SO:0001574\|splice_acceptor_variant
YARS2	chr12	32900620	T	C	single_nucleotide_variant	Benign	not_provided	SO:0001627\|intron_variant	SO:0001627\|intron_variant
YARS2	chr12	32902681	A	ATTT	Duplication	Benign	not_provided	SO:0001627\|intron_variant	SO:0001627\|intron_variant
YARS2	chr12	32902712	C	T	single_nucleotide_variant	Benign	not_provided	SO:0001627\|intron_variant	SO:0001627\|intron_variant
YARS2	chr12	32902874	C	T	single_nucleotide_variant	Uncertain_significance	not_provided	SO:0001583\|missense_variant	SO:0001583\|missense_variant
YARS2	chr12	32902904	C	T	single_nucleotide_variant	Uncertain_significance	Myopathy,_lactic_acidosis,_and_sideroblastic_anemia_2\|Hereditary_Sideroblastic_Anemia_with_Myopathy_and_Lactic_Acidosis	SO:0001583\|missense_variant	SO:0001583\|missense_variant
YARS2	chr12	32902980	A	ACTCCTGATCAGACATGAC	Duplication	Pathogenic	Mitochondrial_disease	SO:0001821\|inframe_insertion	SO:0001821\|inframe_insertion
YARS2	chr12	32903039	C	T	single_nucleotide_variant	Pathogenic	Mitochondrial_disease	SO:0001583\|missense_variant	SO:0001583\|missense_variant
YARS2	chr12	32903053	A	AT	Duplication	Conflicting_interpretations_of_pathogenicity	Mitochondrial_myopathy_and_sideroblastic_anemia\|Hereditary_Sideroblastic_Anemia_with_Myopathy_and_Lactic_Acidosis\|not_provided	SO:0001627\|intron_variant	SO:0001627\|intron_variant
YARS2	chr12	32903148	T	G	single_nucleotide_variant	Benign	not_provided	SO:0001627\|intron_variant	SO:0001627\|intron_variant
YARS2	chr12	32903238	C	T	single_nucleotide_variant	Likely_benign	not_provided	SO:0001627\|intron_variant	SO:0001627\|intron_variant
YARS2	chr12	32903252	C	T	single_nucleotide_variant	Benign	not_provided	SO:0001627\|intron_variant	SO:0001627\|intron_variant
YARS2	chr12	32903331	T	C	single_nucleotide_variant	Likely_benign	not_provided	SO:0001627\|intron_variant	SO:0001627\|intron_variant
YARS2	chr12	32903635	A	G	single_nucleotide_variant	Benign	not_specified	SO:0001627\|intron_variant	SO:0001627\|intron_variant
YARS2	chr12	32903678	G	A	single_nucleotide_variant	Pathogenic	Myopathy,_lactic_acidosis,_and_sideroblastic_anemia_2	SO:0001587\|nonsense	SO:0001587\|nonsense
YARS2	chr12	32903730	C	T	single_nucleotide_variant	Benign/Likely_benign	Myopathy,_lactic_acidosis,_and_sideroblastic_anemia_2\|not_specified\|Hereditary_Sideroblastic_Anemia_with_Myopathy_and_Lactic_Acidosis\|not_provided	SO:0001819\|synonymous_variant	SO:0001819\|synonymous_variant
YARS2	chr12	32903796	C	T	single_nucleotide_variant	Likely_benign	not_specified\|not_provided	SO:0001819\|synonymous_variant	SO:0001819\|synonymous_variant
YARS2	chr12	32903808	C	T	single_nucleotide_variant	Uncertain_significance	not_provided	SO:0001819\|synonymous_variant	SO:0001819\|synonymous_variant
YARS2	chr12	32903828	G	A	single_nucleotide_variant	Likely_benign	not_specified	SO:0001627\|intron_variant	SO:0001627\|intron_variant
YARS2	chr12	32904005	C	CT	Duplication	Benign	not_provided	SO:0001627\|intron_variant	SO:0001627\|intron_variant
YARS2	chr12	32904021	A	G	single_nucleotide_variant	Likely_benign	not_provided	SO:0001627\|intron_variant	SO:0001627\|intron_variant
YARS2	chr12	32904069	T	C	single_nucleotide_variant	Likely_benign	not_provided	SO:0001627\|intron_variant	SO:0001627\|intron_variant
YARS2	chr12	32904089	C	T	single_nucleotide_variant	Benign	not_provided	SO:0001627\|intron_variant	SO:0001627\|intron_variant
YARS2	chr12	32906690	T	C	single_nucleotide_variant	Likely_benign	not_provided	SO:0001627\|intron_variant	SO:0001627\|intron_variant
YARS2	chr12	32906865	C	G	single_nucleotide_variant	Uncertain_significance	Mitochondrial_myopathy_and_sideroblastic_anemia\|Myopathy,_lactic_acidosis,_and_sideroblastic_anemia_2	SO:0001583\|missense_variant	SO:0001583\|missense_variant
YARS2	chr12	32906866	G	C	single_nucleotide_variant	Likely_pathogenic	not_provided	SO:0001583\|missense_variant	SO:0001583\|missense_variant
YARS2	chr12	32906869	C	G	single_nucleotide_variant	Likely_benign	not_provided	SO:0001819\|synonymous_variant	SO:0001819\|synonymous_variant
YARS2	chr12	32906869	C	T	single_nucleotide_variant	Conflicting_interpretations_of_pathogenicity	Myopathy,_lactic_acidosis,_and_sideroblastic_anemia_2\|not_specified\|Hereditary_Sideroblastic_Anemia_with_Myopathy_and_Lactic_Acidosis\|not_provided	SO:0001819\|synonymous_variant	SO:0001819\|synonymous_variant
YARS2	chr12	32906871	G	A	single_nucleotide_variant	Uncertain_significance	not_provided	SO:0001583\|missense_variant	SO:0001583\|missense_variant
YARS2	chr12	32906877	T	G	single_nucleotide_variant	Likely_benign	not_provided	SO:0001819\|synonymous_variant	SO:0001819\|synonymous_variant
YARS2	chr12	32906882	A	G	single_nucleotide_variant	Uncertain_significance	Myopathy,_lactic_acidosis,_and_sideroblastic_anemia_2\|Hereditary_Sideroblastic_Anemia_with_Myopathy_and_Lactic_Acidosis	SO:0001583\|missense_variant	SO:0001583\|missense_variant
YARS2	chr12	32906916	C	T	single_nucleotide_variant	Likely_benign	not_specified	SO:0001583\|missense_variant	SO:0001583\|missense_variant
YARS2	chr12	32906929	A	G	single_nucleotide_variant	Conflicting_interpretations_of_pathogenicity	Mitochondrial_myopathy_and_sideroblastic_anemia\|Myopathy,_lactic_acidosis,_and_sideroblastic_anemia_2\|not_specified\|not_provided	SO:0001819\|synonymous_variant	SO:0001819\|synonymous_variant
YARS2	chr12	32906956	CT	C	Deletion	Pathogenic	not_provided	SO:0001589\|frameshift_variant	SO:0001589\|frameshift_variant
YARS2	chr12	32906980	T	C	single_nucleotide_variant	Conflicting_interpretations_of_pathogenicity	Mitochondrial_myopathy_and_sideroblastic_anemia\|Myopathy,_lactic_acidosis,_and_sideroblastic_anemia_2\|not_specified	SO:0001819\|synonymous_variant	SO:0001819\|synonymous_variant
YARS2	chr12	32906989	G	A	single_nucleotide_variant	Conflicting_interpretations_of_pathogenicity	Myopathy,_lactic_acidosis,_and_sideroblastic_anemia_2\|not_provided	SO:0001819\|synonymous_variant	SO:0001819\|synonymous_variant
YARS2	chr12	32907004	ATCT	A	Microsatellite	Likely_pathogenic	not_provided	SO:0001822\|inframe_deletion	SO:0001822\|inframe_deletion
YARS2	chr12	32907023	C	T	single_nucleotide_variant	Likely_benign	not_provided	SO:0001627\|intron_variant	SO:0001627\|intron_variant
YARS2	chr12	32907172	A	G	single_nucleotide_variant	Likely_benign	not_provided	SO:0001627\|intron_variant	SO:0001627\|intron_variant
YARS2	chr12	32907880	G	A	single_nucleotide_variant	Likely_benign	not_provided	SO:0001627\|intron_variant	SO:0001627\|intron_variant
YARS2	chr12	32907979	G	C	single_nucleotide_variant	Likely_benign	not_provided	SO:0001627\|intron_variant	SO:0001627\|intron_variant
YARS2	chr12	32908058	T	C	single_nucleotide_variant	Likely_pathogenic	Myopathy,_lactic_acidosis,_and_sideroblastic_anemia_2	SO:0001583\|missense_variant	SO:0001583\|missense_variant
YARS2	chr12	32908102	T	C	single_nucleotide_variant	Uncertain_significance	not_provided	SO:0001583\|missense_variant	SO:0001583\|missense_variant
YARS2	chr12	32908122	G	T	single_nucleotide_variant	Uncertain_significance	not_provided	SO:0001583\|missense_variant	SO:0001583\|missense_variant
YARS2	chr12	32908156	T	C	single_nucleotide_variant	Uncertain_significance	Inborn_genetic_diseases	SO:0001583\|missense_variant	SO:0001583\|missense_variant
YARS2	chr12	32908175	C	A	single_nucleotide_variant	Likely_pathogenic	not_provided	SO:0001587\|nonsense	SO:0001587\|nonsense
YARS2	chr12	32908183	T	C	single_nucleotide_variant	Conflicting_interpretations_of_pathogenicity	Myopathy,_lactic_acidosis,_and_sideroblastic_anemia_2\|Hereditary_Sideroblastic_Anemia_with_Myopathy_and_Lactic_Acidosis\|not_provided	SO:0001583\|missense_variant	SO:0001583\|missense_variant
YARS2	chr12	32908192	A	AG	Duplication	Likely_pathogenic	not_provided	SO:0001589\|frameshift_variant	SO:0001589\|frameshift_variant
YARS2	chr12	32908237	C	A	single_nucleotide_variant	Benign/Likely_benign	Mitochondrial_myopathy_and_sideroblastic_anemia\|Myopathy,_lactic_acidosis,_and_sideroblastic_anemia_2\|not_provided	SO:0001583\|missense_variant	SO:0001583\|missense_variant
YARS2	chr12	32908237	C	T	single_nucleotide_variant	Pathogenic	Myopathy,_lactic_acidosis,_and_sideroblastic_anemia_2	SO:0001583\|missense_variant	SO:0001583\|missense_variant
YARS2	chr12	32908256	A	G	single_nucleotide_variant	Likely_pathogenic	not_provided	SO:0001583\|missense_variant	SO:0001583\|missense_variant
YARS2	chr12	32908274	T	G	single_nucleotide_variant	Conflicting_interpretations_of_pathogenicity	Myopathy,_lactic_acidosis,_and_sideroblastic_anemia_2\|not_specified\|Hereditary_Sideroblastic_Anemia_with_Myopathy_and_Lactic_Acidosis	SO:0001583\|missense_variant	SO:0001583\|missense_variant
YARS2	chr12	32908287	C	G	single_nucleotide_variant	Likely_benign	not_provided	SO:0001819\|synonymous_variant	SO:0001819\|synonymous_variant
YARS2	chr12	32908332	G	A	single_nucleotide_variant	Conflicting_interpretations_of_pathogenicity	Myopathy,_lactic_acidosis,_and_sideroblastic_anemia_2\|not_specified\|Hereditary_Sideroblastic_Anemia_with_Myopathy_and_Lactic_Acidosis	SO:0001819\|synonymous_variant	SO:0001819\|synonymous_variant
YARS2	chr12	32908353	C	T	single_nucleotide_variant	Conflicting_interpretations_of_pathogenicity	Myopathy,_lactic_acidosis,_and_sideroblastic_anemia_2\|not_specified\|Hereditary_Sideroblastic_Anemia_with_Myopathy_and_Lactic_Acidosis\|not_provided	SO:0001819\|synonymous_variant	SO:0001819\|synonymous_variant
YARS2	chr12	32908392	G	A	single_nucleotide_variant	Likely_benign	not_provided	SO:0001819\|synonymous_variant	SO:0001819\|synonymous_variant
YARS2	chr12	32908435	C	G	single_nucleotide_variant	Likely_pathogenic	not_provided	SO:0001583\|missense_variant	SO:0001583\|missense_variant
YARS2	chr12	32908449	T	TC	Duplication	Pathogenic	Myopathy,_lactic_acidosis,_and_sideroblastic_anemia_2	SO:0001589\|frameshift_variant	SO:0001589\|frameshift_variant
YARS2	chr12	32908467	G	A	single_nucleotide_variant	Benign	not_specified\|not_provided	SO:0001819\|synonymous_variant	SO:0001819\|synonymous_variant
YARS2	chr12	32908482	G	C	single_nucleotide_variant	Uncertain_significance	Myopathy,_lactic_acidosis,_and_sideroblastic_anemia_2\|Hereditary_Sideroblastic_Anemia_with_Myopathy_and_Lactic_Acidosis	SO:0001583\|missense_variant	SO:0001583\|missense_variant
YARS2	chr12	32908518	G	A	single_nucleotide_variant	Benign/Likely_benign	Myopathy,_lactic_acidosis,_and_sideroblastic_anemia_2\|not_specified\|Hereditary_Sideroblastic_Anemia_with_Myopathy_and_Lactic_Acidosis\|not_provided	SO:0001819\|synonymous_variant	SO:0001819\|synonymous_variant
YARS2	chr12	32908529	C	T	single_nucleotide_variant	Uncertain_significance	not_provided	SO:0001583\|missense_variant	SO:0001583\|missense_variant
YARS2	chr12	32908573	C	A	single_nucleotide_variant	Likely_pathogenic	not_provided	SO:0001583\|missense_variant	SO:0001583\|missense_variant
YARS2	chr12	32908575	A	G	single_nucleotide_variant	Uncertain_significance	Myopathy,_lactic_acidosis,_and_sideroblastic_anemia_2\|Hereditary_Sideroblastic_Anemia_with_Myopathy_and_Lactic_Acidosis	SO:0001819\|synonymous_variant	SO:0001819\|synonymous_variant
YARS2	chr12	32908584	G	A	single_nucleotide_variant	Likely_benign	not_provided	SO:0001819\|synonymous_variant	SO:0001819\|synonymous_variant
YARS2	chr12	32908607	C	CA	Duplication	Likely_pathogenic	not_provided	SO:0001589\|frameshift_variant	SO:0001589\|frameshift_variant
YARS2	chr12	32908607	C	T	single_nucleotide_variant	Conflicting_interpretations_of_pathogenicity	Myopathy,_lactic_acidosis,_and_sideroblastic_anemia_2\|not_specified	SO:0001583\|missense_variant	SO:0001583\|missense_variant
YARS2	chr12	32908628	G	C	single_nucleotide_variant	Likely_pathogenic	not_provided	SO:0001583\|missense_variant	SO:0001583\|missense_variant
YARS2	chr12	32908629	C	T	single_nucleotide_variant	Uncertain_significance	Mitochondrial_myopathy_and_sideroblastic_anemia\|Myopathy,_lactic_acidosis,_and_sideroblastic_anemia_2	SO:0001819\|synonymous_variant	SO:0001819\|synonymous_variant
YARS2	chr12	32908653	G	C	single_nucleotide_variant	Pathogenic/Likely_pathogenic	Myopathy,_lactic_acidosis,_and_sideroblastic_anemia_2\|not_provided	SO:0001583\|missense_variant	SO:0001583\|missense_variant
YARS2	chr12	32908672	C	T	single_nucleotide_variant	Pathogenic	Myopathy,_lactic_acidosis,_and_sideroblastic_anemia_2\|not_provided	SO:0001583\|missense_variant	SO:0001583\|missense_variant
YARS2	chr12	32908705	G	T	single_nucleotide_variant	Conflicting_interpretations_of_pathogenicity	Myopathy,_lactic_acidosis,_and_sideroblastic_anemia_2\|not_specified\|Hereditary_Sideroblastic_Anemia_with_Myopathy_and_Lactic_Acidosis\|not_provided	SO:0001583\|missense_variant	SO:0001583\|missense_variant
YARS2	chr12	32908779	G	A	single_nucleotide_variant	Uncertain_significance	Myopathy,_lactic_acidosis,_and_sideroblastic_anemia_2\|Hereditary_Sideroblastic_Anemia_with_Myopathy_and_Lactic_Acidosis	SO:0001819\|synonymous_variant	SO:0001819\|synonymous_variant
YARS2	chr12	32908839	T	C	single_nucleotide_variant	Uncertain_significance	Myopathy,_lactic_acidosis,_and_sideroblastic_anemia_2	SO:0002153\|genic_upstream_transcript_variant	SO:0002153\|genic_upstream_transcript_variant
YARS2	chr12	32908880	G	C	single_nucleotide_variant	Uncertain_significance	Myopathy,_lactic_acidosis,_and_sideroblastic_anemia_2	SO:0002153\|genic_upstream_transcript_variant	SO:0002153\|genic_upstream_transcript_variant
YARS2	chr12	32908961	C	G	single_nucleotide_variant	Benign	not_provided	SO:0002153\|genic_upstream_transcript_variant	SO:0002153\|genic_upstream_transcript_variant

nsSNVs with sample frequency (size of circle) from TCGA 33 cancers.

SNVs and Indels

Gene	Cancer type	Chromosome	Start	End	RefSeeq	MutSeq	Mutation type	AAchange	# samples
YARS2	LUAD	chr12	32908775	32908775	C	A	Missense_Mutation	p.G12C	7
YARS2	ESCA	chr12	32908804	32908804	G	T	Missense_Mutation	p.A2E	3
YARS2	BLCA	chr12	32906904	32906904	G	A	Missense_Mutation		3
YARS2	LUAD	chr12	32908428	32908428	C	G	Missense_Mutation	p.K127N	3
YARS2	UCS	chr12	32908477	32908477	A	C	Missense_Mutation	p.L111R	3
YARS2	HNSC	chr12	32908286	32908286	C	A	Missense_Mutation	p.A175S	3
YARS2	BRCA	chr12	32908185	32908185	G	A	Silent	p.L208	3
YARS2	KIRP	chr12	32908454	32908454	G	-	Frame_Shift_Del	p.L119fs	3
YARS2	BLCA	chr12	32906904	32906904	G	A	Missense_Mutation	p.P299S	3
YARS2	UCEC	chr12	32906877	32906877	T	C	Missense_Mutation	p.R308G	3
YARS2	ESCA	chr12	32908126	32908126	T	C	Missense_Mutation	p.D228G	3
YARS2	UCEC	chr12	32903673	32903673	T	C	Silent	p.E361	2
YARS2	SARC	chr12	32908155	32908155	C	A	Missense_Mutation	p.E218D	2
YARS2	UCEC	chr12	32906906	32906906	G	A	Missense_Mutation	p.S298F	2
YARS2	ESCA	chr12	32908126	32908126	T	C	Missense_Mutation		2
YARS2	SARC	chr12	32908628	32908628	G	A	Missense_Mutation	p.L61F	2
YARS2	TGCT	chr12	32908276	32908276	T	C	Missense_Mutation		2
YARS2	PRAD	chr12	32902905	32902905	G	A	Missense_Mutation	p.R414C	2
YARS2	UCEC	chr12	32908751	32908751	G	T	Missense_Mutation	p.L20I	2
YARS2	ESCA	chr12	32908804	32908804	G	T	Missense_Mutation		2
YARS2	SKCM	chr12	32900275	32900275	C	T	Missense_Mutation	p.G433R	2
YARS2	COAD	chr12	32900293	32900293	G	A	Nonsense_Mutation	p.R427X	2
YARS2	TGCT	chr12	32908276	32908276	T	C	Missense_Mutation	p.Q178R	2
YARS2	HNSC	chr12	32900172	32900172	C	T	Missense_Mutation	p.R467K	2
YARS2	SKCM	chr12	32908665	32908665	G	A	Silent	p.F48F	2
YARS2	LIHC	chr12	32908593	32908593	A	-	Frame_Shift_Del	p.F72fs	2
YARS2	HNSC	chr12	32903773	32903773	T	A	Missense_Mutation	p.E328V	2
YARS2	STAD	chr12	32908208	32908208	G	A	Missense_Mutation		2
YARS2	THYM	chr12	32908584	32908584	G	A	Silent		2
YARS2	SARC	chr12	32902898	32902898	G	T	Missense_Mutation		2
YARS2	STAD	chr12	32908785	32908785	G	T	Silent		2
YARS2	THYM	chr12	32908584	32908584	G	A	Silent	p.T75T	2
YARS2	BRCA	chr12	32903765	32903765	G	A	Missense_Mutation	p.H331Y	2
YARS2	STAD	chr12	32908785	32908785	G	T	Silent	p.S8S	2
YARS2	SARC	chr12	32908628	32908628	G	A	Missense_Mutation		2
YARS2	STAD	chr12	32908208	32908208	G	A	Missense_Mutation	p.R201W	2
YARS2	SARC	chr12	32908155	32908155	C	A	Missense_Mutation		2
YARS2	STAD	chr12	32908614	32908614	G	A	Silent	p.F65F	2
YARS2	CESC	chr12	32908137	32908137	G	C	Silent		2
YARS2	OV	chr12	32799342	32799342	G	C	Missense_Mutation	p.S245C	1
YARS2	BLCA	chr12	32903720	32903720	G	A	Nonsense_Mutation	p.Q346*	1
YARS2	HNSC	chr12	32908353	32908353	C	T	Silent		1
YARS2	CESC	chr12	32906904	32906904	G	C	Missense_Mutation	p.P299A	1
YARS2	LIHC	chr12	32908518	32908518	G	A	Silent		1
YARS2	LUAD	chr12	32908396	32908396	C	T	Missense_Mutation	p.R138Q	1
YARS2	STAD	chr12	32908133	32908133	C	T	Missense_Mutation	p.A226T	1
YARS2	PAAD	chr12	32908717	32908717	G	T	Missense_Mutation	p.A31D	1
YARS2	BLCA	chr12	32903776	32903776	G	A	Missense_Mutation	p.P327L	1
YARS2	HNSC	chr12	32903678	32903678	G	C	Missense_Mutation	p.R360G	1
YARS2	CESC	chr12	32908137	32908137	G	C	Silent	p.L224	1
YARS2	LIHC	chr12	32903790	32903790	A	G	Silent		1
YARS2	LUAD	chr12	32906891	32906891	T	C	Missense_Mutation	p.Y303C	1
YARS2	BLCA	chr12	32908711	32908711	G	A	Missense_Mutation	p.S33L	1
YARS2	HNSC	chr12	32908353	32908353	C	T	Silent	p.A152A	1
YARS2	LIHC	chr12	32908049	32908049	C	T	Missense_Mutation		1
YARS2	PRAD	chr12	32903660	32903660	C	T	Missense_Mutation	p.A366T	1
YARS2	UCS	chr12	32908477	32908477	A	C	Missense_Mutation		1
YARS2	BLCA	chr12	32908656	32908656	G	T	Missense_Mutation		1
YARS2	ESCA	chr12	32908115	32908115	G	T	Missense_Mutation	p.L232I	1
YARS2	BLCA	chr12	32908693	32908693	A	C	Missense_Mutation	p.L39R	1
YARS2	COAD	chr12	32900296	32900296	A	C	Missense_Mutation	p.Y426D	1
YARS2	LUAD	chr12	32908175	32908175	C	T	Missense_Mutation	p.E212K	1
YARS2	THYM	chr12	32906878	32906878	G	T	Silent		1
YARS2	PRAD	chr12	32903729	32903729	G	A	Missense_Mutation	p.R343W	1
YARS2	BLCA	chr12	32903776	32903776	G	A	Missense_Mutation		1
YARS2	GBM	chr12	32908585	32908585	G	C	Missense_Mutation	p.T75S	1
YARS2	BLCA	chr12	32903745	32903745	G	C	Silent	p.V337V	1
YARS2	SKCM	chr12	32908768	32908768	C	T	Nonsense_Mutation	p.W14*	1
YARS2	COAD	chr12	32902924	32902924	T	C	Silent	p.T407T	1
YARS2	LIHC	chr12	32900173	32900173	T	-	Frame_Shift_Del	p.R467fs	1
YARS2	LUAD	chr12	32907006	32907006	C	G	Missense_Mutation	p.D265H	1
YARS2	THYM	chr12	32908551	32908551	C	T	Silent		1
YARS2	READ	chr12	32903713	32903713	C	T	Missense_Mutation	p.R348Q	1
YARS2	BLCA	chr12	32908711	32908711	G	A	Missense_Mutation		1
YARS2	GBM	chr12	32908585	32908585	G	C	Missense_Mutation		1
YARS2	BLCA	chr12	32908665	32908665	G	C	Missense_Mutation	p.F48L	1
YARS2	COAD	chr12	32903721	32903721	A	G	Silent	p.P345P	1
YARS2	LIHC	chr12	32908728	32908728	C	-	Frame_Shift_Del	p.G27fs	1
YARS2	LUAD	chr12	32908421	32908421	C	T	Missense_Mutation	p.E130K	1
YARS2	BLCA	chr12	32908693	32908693	A	C	Missense_Mutation		1
YARS2	HNSC	chr12	32903773	32903773	T	A	Missense_Mutation		1
YARS2	BLCA	chr12	32908747	32908747	G	C	Nonsense_Mutation	p.S21*	1
YARS2	KIRC	chr12	32908125	32908125	G	C	Missense_Mutation	p.D228E	1
YARS2	COAD	chr12	32906951	32906951	C	T	Missense_Mutation	p.G283E	1
YARS2	LUAD	chr12	32908772	32908772	G	A	Missense_Mutation	p.R13W	1
YARS2	LUSC	chr12	32906869	32906869	C	A	Silent	p.P310P	1
YARS2	SARC	chr12	32908678	32908678	G	T	Missense_Mutation		1
YARS2	BLCA	chr12	32903745	32903745	G	C	Silent		1
YARS2	HNSC	chr12	32900172	32900172	C	T	Missense_Mutation		1
YARS2	KIRC	chr12	32900186	32900186	A	T	Silent	p.L462L	1
YARS2	COAD	chr12	32908237	32908237	C	A	Missense_Mutation	p.G191V	1
YARS2	LUSC	chr12	32902909	32902909	A	G	Silent	p.T412T	1
YARS2	THYM	chr12	32906934	32906934	C	T	Missense_Mutation	p.A289T	1
YARS2	BLCA	chr12	32908665	32908665	G	C	Missense_Mutation		1
YARS2	HNSC	chr12	32908286	32908286	C	A	Missense_Mutation		1
YARS2	THYM	chr12	32908584	32908584	G	A	Silent	p.T75	1
YARS2	COAD	chr12	32908518	32908518	G	A	Silent	p.G97G	1
YARS2	LUAD	chr12	32908436	32908436	G	A	Missense_Mutation	p.R125C	1
YARS2	LUSC	chr12	32906940	32906940	C	A	Missense_Mutation	p.G287C	1
YARS2	HNSC	chr12	32903678	32903678	G	C	Missense_Mutation		1
YARS2	CESC	chr12	32906939	32906939	C	A	Missense_Mutation		1
YARS2	LIHC	chr12	32900280	32900280	T	C	Missense_Mutation		1
YARS2	LUSC	chr12	32900274	32900274	C	G	Missense_Mutation	p.G433A	1
YARS2	LUAD	chr12	32908789	32908789	C	G	Missense_Mutation	p.R7P	1
YARS2	BLCA	chr12	32908656	32908656	G	T	Missense_Mutation	p.F51L	1
YARS2	HNSC	chr12	32900275	32900275	C	T	Missense_Mutation		1
YARS2	SARC	chr12	32908271	32908271	G	T	Missense_Mutation		1
YARS2	LIHC	chr12	32908237	32908237	C	A	Missense_Mutation		1
YARS2	STAD	chr12	32902887	32902887	G	A	Missense_Mutation	p.P420S	1

Copy number variation (CNV) of YARS2
* Click on the image to open the original image in a new window.

Fusion gene breakpoints (product of the structural variants (SVs)) across YARS2
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

Fusion genes with this translation factor from FusionGDB2.0.

FusionGDB2 ID	Disease	Sample	Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand
96551	N/A	CA413140	C1orf174	chr1	3806012	+	YARS2	chr12	32897372	-
96551	N/A	EC575602	PECR	chr2	216910909	-	YARS2	chr12	32906889	-
96551	N/A	AA663785	TPCN1	chr12	113698239	+	YARS2	chr12	32908278	-
96551	N/A	AW075450	UCHL1	chr4	41270232	-	YARS2	chr12	32908820	-
99905	N/A	CB050635	YARS2	chr12	32878181	-	C9orf152	chr9	112956266	+
99905	N/A	DA736127	YARS2	chr12	32879412	-	GPX8	chr5	54460646	+
102666	N/A	DM016499	YARS2	chr12	32878165	-	NAP1L1	chr12	76442246	-
100120	OV	TCGA-13-1495-01A	YARS2	chr12	32906852	-	PKP2	chr12	33047712	-

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Prognostic Analysis

Kaplan-Meier plots with logrank tests of overall survival (OS)

Cancer type

Translation factor

Coefficent

Hazard ratio

Wald test pval

Likelihool ratio pval

Logrank test pval

# samples

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Translation factor and Gender

Differential gene expression between female and male. (Wilcoxon test, pval<0.05)

Cancer type	Translation factor	pval	adj.p
LUSC	YARS2	0.000554471567911417	0.016
READ	YARS2	0.0137474171488708	0.37
ESCA	YARS2	0.0184243279120372	0.48
LUAD	YARS2	0.0208731193617442	0.52
STAD	YARS2	0.0257816133642537	0.62

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Translation factor and Age

Differential gene expression between young and old age groups (Wilcoxon test, pval<0.05)

Cancer type	Translation factor	pval	adj.p
LUSC	YARS2	0.00563857017959976	0.17
LAML	YARS2	0.0191490733299495	0.57
BRCA	YARS2	0.000682715478550158	0.023
UCEC	YARS2	0.0339417409532565	0.98
ESCA	YARS2	0.00285947520504662	0.092
THYM	YARS2	0.0424012669591162	1

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Related Drugs

Drugs targeting genes involved in this translation factor.
(DrugBank Version 5.1.8 2021-05-08)

UniProtAcc

DrugBank ID

Drug name

Drug activity

Drug type

Drug status

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Related Diseases

Diseases associated with this translation factor.
(DisGeNet 4.0)

Disease ID	Disease Name	# PubMeds	Disease source
C3150802	MYOPATHY, LACTIC ACIDOSIS, AND SIDEROBLASTIC ANEMIA 2	5	GENOMICS_ENGLAND;UNIPROT
C1838103	MITOCHONDRIAL MYOPATHY AND SIDEROBLASTIC ANEMIA	4	CTD_human;ORPHANET