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Center for Computational Systems Medicine
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Gene Summary

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Translation studies in PubMed

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Exon Skipping Events

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Expression

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Expression Regulation

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Associated Genes

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Protein 3D Structure

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Protein-Protein Interaction

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Mutations

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Prognostic Analysis

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Gender Association

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Age Association

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Related Drugs

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Related Diseases

Translation Factor: TRMT10C (NCBI Gene ID:54931)


Gene Summary

check button Gene Summary
Gene InformationGene Name: TRMT10C
Gene ID: 54931
Gene Symbol

TRMT10C

Gene ID

54931

Gene NametRNA methyltransferase 10C, mitochondrial RNase P subunit
SynonymsCOXPD30|HNYA|MRPP1|RG9MTD1
Cytomap

3q12.3

Type of Geneprotein-coding
DescriptiontRNA methyltransferase 10 homolog CHBV pre-S2 trans-regulated protein 2RNA (guanine-9-) methyltransferase domain containing 1mRNA methyladenosine-N(1)-methyltransferasemitochondrial RNase P subunit 1mitochondrial ribonuclease P protein 1renal carcin
Modification date20200313
UniProtAcc

Q7L0Y3


check button Child GO biological process term(s) under GO:0006412
GO IDGO term
GO:0006417Regulation of translation
GO:0032543Mitochondrial translation
GO:0045727Positive regulation of translation
GO:0006412Translation


check button Gene ontology of translaction factor with evidence of Inferred from Direct Assay (IDA) from Entrez
PartnerGeneGO IDGO termPubMed ID
HgeneTRMT10C

GO:0080009

mRNA methylation

29072297

HgeneTRMT10C

GO:0097745

mitochondrial tRNA 5'-end processing

29040705

HgeneTRMT10C

GO:1990180

mitochondrial tRNA 3'-end processing

29040705



check button Inferred gene age of translation factor.
GeneInferred gene age group among (0 - 67.6], (67.6 - 355.7], (355.7 - 733], (733 - 1119.25], >1119.25
TRMT10C(733 - 1119.25]


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Translation Studies in PubMed

check button We searched PubMed using 'TRMT10C[title] AND translation [title] AND human.'
GeneTitlePMID
TRMT10C..


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Exon Skipping Events

check buttonSkipped 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.
all structure

check button 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.
ENSTExon skip start (DNA)Exon Skip end (DNA)ORF

check button Exon skipping position in the amino acid sequence.
ENSTExon 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)

check button Potentially (partially) lost protein functional features of UniProt.
UniProtAccExon skip start (AA)Exon Skip end (AA)Function feature start (AA)Function feature end (AA)Functional feature typeFunctional feature desc.


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Expression


check buttonGene expression level across TCGA pancancer
all structure

check buttonGene expression level across GTEx pantissue
all structure

check buttonExpression level of gene isoforms across TCGA pancancer
all structure

check buttonExpression level of gene isoforms across GTEx pantissue
all structure

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

check buttonDifferential expression between tumor and matched normal (in the cancer types with more than 10 matched samples)
Cancer typeTranslation factorFCadj.pval


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Expression Regulation


check buttonTranslation factor expression regulation through miRNA binding
Cancer typeGenemiRNATargetScan binding score (Context++ score percentile)CoefficientPvalue


check buttonTranslation factor expression regulation through methylation in the promoter of Translation factor
Cancer typeGenemethyl group bmethyl group aDEG pvalavg methyl in bavg methyl in aavg exp in bavg exp in a

check buttonTranslation factor expression regulation through methylation in the gene body of Translation factor (positive regulation)
Cancer typeGenemethyl group bmethyl group aDEG pvalavg methyl in bavg methyl in aavg exp in bavg exp in a

check buttonTranslation factor expression regulation through copy number variation of Translation factor
Cancer typeGeneCoefficientPvalue

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Associated Genes


check button Strongly correlated genes belong to cellular important gene groups with TRMT10C (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 typeGene groupTranslation factorCorrelated geneCoefficientPvalue


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Protein structure


check button Protein 3D structure
Visit iCn3D.


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Protein-Protein Interaction


check button 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))
all structure

check buttonOverlap 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))
all structure
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* Edge colors based on TCGA cancer types.

check button* 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))
all structure
Cancer typeTranslation factorInteracting protein coding geneFCadj.pval
LUSCTRMT10CELAC2-1.349953051070760.000173983823784929
KIRPTRMT10CTRMT51.325302169692520.000177780166268349
KIRPTRMT10CTRMT62.386338227418320.000306400004774332
KIRCTRMT10CMRM1-1.07529673607360.000369980864421695
LUSCTRMT10CGRSF1-2.762478965715290.00051492571390515
COADTRMT10CMRM11.239392014167860.000934779644012452
ESCATRMT10CTRMT6-3.116777662470450.0009765625
THCATRMT10CGRSF1-1.089410765874450.00125200545023797
PRADTRMT10CHSD17B10-1.954561080170680.0028589043032549
CHOLTRMT10CHSD17B10-7.552778749191550.00390625
THCATRMT10CELAC2-2.690235195986670.00492925389458784
KIRPTRMT10CKIAA0391-3.306166326652540.00647870777174831
ESCATRMT10CMRM1-1.223443938584780.013671875
STADTRMT10CGRSF1-1.479849516592370.0265949876047671
HNSCTRMT10CMRM1-1.325652853345560.0341586761198869
LUADTRMT10CMRM1-2.803869039759051.0542655358657e-09
BRCATRMT10CTRMT5-1.869611972933061.08510546514812e-15
STADTRMT10CTRMT6-5.428634702826061.42958015203476e-07
BRCATRMT10CFSIP11.004899291127051.50831824899887e-08
LUADTRMT10CPUS1-2.331498162499261.55042044095848e-09
KICHTRMT10CPUS1-1.078309724914591.82986259460449e-05
LUSCTRMT10CMRM1-4.212369790580362.79558697199975e-08
LIHCTRMT10CTRMT6-1.330495437426133.4520382341717e-07
KIRCTRMT10CKIAA0391-2.511263742332363.45880777969452e-10
KIRPTRMT10CELAC22.129361062786434.57269180191994e-05
LUADTRMT10CGRSF1-2.606146244717384.74567569196557e-06
KIRCTRMT10CFSIP1-1.003013371881834.88225501247017e-07
LUADTRMT10CTRMT61B-2.531281394097855.01965000240228e-08
LUSCTRMT10CHSD17B10-4.273446479646895.28938905102431e-08
BRCATRMT10CHSD17B10-2.348844759385825.38451702044162e-16
LUADTRMT10CTRMT5-5.37158617369515.47570214265305e-08
THCATRMT10CTRMT61B1.963556033452576.64269613223191e-08
KIRPTRMT10CPUS1-4.44191193042758.84756445884705e-09
LUADTRMT10CHSD17B10-1.481990310246539.53955602455483e-07
KIRPTRMT10CFSIP1-1.150357715100899.90275293588639e-06


check button Protein-protein interactors with this translation factor (BIOGRID-3.4.160)
PPI interactors with TRMT10C
USP39, HDGF, CUL3, CAND1, ASB1, GRSF1, CEP57, CEP76, TP53, EGFR, TRNI, ZZEF1, HECTD3, NTRK1, NOP56, Cct3, Eif3a, Smc1a, Rpl35, Gtf3c4, Mdm2, POU5F1, CHCHD2, CISD3, C15orf48, TPTE, DUSP26, VWA5A, ELAC2, TRNT1, HSD17B10, DLD, HIF1AN, EGLN3, UBE2M, EFTUD2, ESR2, HEXIM1, MEPCE, LARP7, SNAI1, RECQL4, HABP4, SERBP1, SOCS1, AIFM1, BET1, MRM1, HSPD1, PDK1, TRMT61B, AURKAIP1, USP14, NR2C2, TCF7L2, SNRNP70, PTPRU, BIRC3, PLEKHA4, MIRLET7A3, MIR15A, FGFR1, EMC4, PARL, E, nsp16, nsp9, ORF6, ESR1, CIT, ANLN, KIF14, KIF23, ARHGEF10L, ACAD9, AUH, C12orf65, C1QBP, C21orf33, C6orf203, MCUR1, CCDC90B, CHCHD1, CS, DDX28, DHX30, FASTKD2, FASTKD3, FASTKD5, GFM1, GFM2, HINT2, ICT1, LONP1, LRPPRC, CCDC109B, MDH2, METTL15, METTL17, MRPL11, MRPS12, MRPS26, MRRF, MTERF3, MTFMT, MTG1, MTG2, MTIF2, MTIF3, MTRF1, MTRF1L, NGRN, OTC, PMPCA, PMPCB, RPUSD3, RPUSD4, SLIRP, SSBP1, TACO1, TBRG4, TEFM, TFAM, TMEM70, TRUB2, TSFM, TUFM, VWA8, EXD2, CLPP, Apc2, FBP1, LGALS9, DNAJC15, DNAJC19, DNAJC28, HSCB, HSPA9, OGT, UFL1, DDRGK1, AARS2, AKAP1, COX8A, PDHA1, RHOB, TRAP1, FZR1, FBXW7, DPP4, TMPRSS4, MAP1LC3B,


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Mutations


check button Clinically associated variants from ClinVar.
GeneChrPositionRefSeqVarSeqRefSeeqVarTypePathogenicDiseaseVarInfo
TRMT10Cchr3101283792CGsingle_nucleotide_variantBenignnot_providedSO:0001583|missense_variantSO:0001583|missense_variant
TRMT10Cchr3101284039GAsingle_nucleotide_variantLikely_benignnot_providedSO:0001819|synonymous_variantSO:0001819|synonymous_variant
TRMT10Cchr3101284117GCsingle_nucleotide_variantBenign/Likely_benignnot_providedSO:0001583|missense_variantSO:0001583|missense_variant
TRMT10Cchr3101284119TAsingle_nucleotide_variantLikely_benignnot_providedSO:0001583|missense_variantSO:0001583|missense_variant
TRMT10Cchr3101284167GTsingle_nucleotide_variantPathogenicCombined_oxidative_phosphorylation_deficiency_30|Mitochondrial_diseaseSO:0001583|missense_variantSO:0001583|missense_variant
TRMT10Cchr3101284414AGsingle_nucleotide_variantLikely_benignnot_providedSO:0001819|synonymous_variantSO:0001819|synonymous_variant
TRMT10Cchr3101284439AGsingle_nucleotide_variantPathogenicCombined_oxidative_phosphorylation_deficiency_30|Mitochondrial_diseaseSO:0001583|missense_variantSO:0001583|missense_variant
TRMT10Cchr3101284747AGsingle_nucleotide_variantLikely_benignnot_providedSO:0001819|synonymous_variantSO:0001819|synonymous_variant
TRMT10Cchr3101284750CTsingle_nucleotide_variantLikely_benignnot_providedSO:0001819|synonymous_variantSO:0001819|synonymous_variant
TRMT10Cchr3101284940TCsingle_nucleotide_variantBenignnot_providedSO:0001624|3_prime_UTR_variantSO:0001624|3_prime_UTR_variant


check button nsSNVs with sample frequency (size of circle) from TCGA 33 cancers.
all structure


check button SNVs and Indels
GeneCancer typeChromosomeStartEndRefSeeqMutSeqMutation typeAAchange# samples
TRMT10CBLCAchr3101284009101284009A-Frame_Shift_Delp.A128fs13
TRMT10CLIHCchr3101283884101283884GAMissense_Mutationp.D87N4
TRMT10CBLCAchr3101283942101283942GCMissense_Mutationp.R106T4
TRMT10CESCAchr3101284019101284019TCMissense_Mutationp.Y132H3
TRMT10CESCAchr3101284219101284219CTSilentp.A198A3
TRMT10CLIHCchr3101283884101283884GAMissense_Mutation3
TRMT10CUCSchr3101284157101284157CAMissense_Mutationp.L178I3
TRMT10CLUADchr3101284693101284693GTMissense_Mutationp.M356I2
TRMT10CKIRPchr3101284214101284214CTNonsense_Mutationp.Q197X2
TRMT10CESCAchr3101283646101283646GTMissense_Mutationp.M7I2
TRMT10CKIRPchr3101284160101284160T-Frame_Shift_Delp.L178fs2
TRMT10CLIHCchr3101283748101283748T-Frame_Shift_Delp.S42fs2
TRMT10CPAADchr3101284007101284007GTMissense_Mutation2
TRMT10CKIRPchr3101284214101284214CTNonsense_Mutation2
TRMT10CCESCchr3101283864101283864CTMissense_Mutation2
TRMT10CCESCchr3101284448101284448GAMissense_Mutation2
TRMT10CSKCMchr3101284528101284528CTSilentp.F301F2
TRMT10CBLCAchr3101283942101283942GCMissense_Mutation2
TRMT10CCESCchr3101283864101283864CTMissense_Mutationp.S80L2
TRMT10CLUADchr3101283774101283774CTMissense_Mutationp.P50L2
TRMT10CHNSCchr3101283915101283915TGMissense_Mutationp.F97C2
TRMT10CSKCMchr3101284124101284124GAMissense_Mutationp.E167K2
TRMT10CHNSCchr3101283935101283935CTMissense_Mutationp.L104F2
TRMT10CSKCMchr3101284252101284252GAMissense_Mutationp.M209I2
TRMT10CBLCAchr3101283784101283784GCMissense_Mutation1
TRMT10CLIHCchr3101284095101284095GTMissense_Mutationp.R157M1
TRMT10CESCAchr3101284009101284009A-Frame_Shift_Delp.K131fs1
TRMT10CLUADchr3101283658101283658CTSilentp.V11V1
TRMT10CHNSCchr3101284667101284667ATMissense_Mutationp.N348Y1
TRMT10CSKCMchr3101283794101283794CTMissense_Mutationp.P57S1
TRMT10CBLCAchr3101284754101284754CGMissense_Mutationp.P377A1
TRMT10CSKCMchr3101283793101283793CTSilentp.P56P1
TRMT10CLIHCchr3101284684101284684AGSilentp.L353L1
TRMT10CLUADchr3101284217101284217GCMissense_Mutationp.A198P1
TRMT10CSTADchr3101284689101284689AGMissense_Mutationp.Q355R1
TRMT10CBLCAchr3101284332101284332GTMissense_Mutationp.R236I1
TRMT10CESCAchr3101284219101284219CTSilent1
TRMT10CSTADchr3101283802101283802AGSilentp.E59E1
TRMT10CSTADchr3101284403101284403A-Frame_Shift_Delp.V259fs1
TRMT10CBLCAchr3101283784101283784GCMissense_Mutationp.E53D1
TRMT10CLIHCchr3101283776101283776A-Frame_Shift_Delp.K51fs1
TRMT10CPAADchr3101284213101284213CTSilent1
TRMT10CLGGchr3101284512101284512AGMissense_Mutationp.N296S1
TRMT10CSTADchr3101284698101284698GAMissense_Mutationp.R358H1
TRMT10CBLCAchr3101283718101283722TAACT-Frame_Shift_Delp.NL32fs1
TRMT10CLIHCchr3101283824101283824A-Frame_Shift_Delp.K67fs1
TRMT10CESCAchr3101284019101284019TCMissense_Mutation1
TRMT10CPAADchr3101284007101284007GTMissense_Mutationp.A128S1
TRMT10CLGGchr3101283849101283851AAG-In_Frame_Delp.QE75del1
TRMT10CLIHCchr3101283661101283661T-Frame_Shift_Delp.N12fs1
TRMT10CTHYMchr3101284320101284320GTMissense_Mutation1
TRMT10CHNSCchr3101283915101283915TGMissense_Mutation1
TRMT10CPRADchr3101284665101284665GTMissense_Mutationp.G347V1
TRMT10CBLCAchr3101284754101284754CGMissense_Mutation1
TRMT10CLIHCchr3101283849101283849A-Frame_Shift_Delp.Q75fs1
TRMT10CTHYMchr3101284320101284320GTMissense_Mutationp.G232V1
TRMT10CHNSCchr3101283935101283935CTMissense_Mutation1
TRMT10CSARCchr3101283705101283705ATMissense_Mutation1
TRMT10CBLCAchr3101283718101283722TAACT-Frame_Shift_Del1
TRMT10CLIHCchr3101283980101283980AGMissense_Mutation1
TRMT10CLIHCchr3101283791101283791C-Frame_Shift_Delp.P57fs1
TRMT10CUCSchr3101284157101284157CAMissense_Mutation1
TRMT10CHNSCchr3101284667101284667ATMissense_Mutation1
TRMT10CLIHCchr3101283690101283690TCMissense_Mutation1
TRMT10CBLCAchr3101284332101284332GTMissense_Mutation1
TRMT10CLIHCchr3101284816101284816AGSilentp.R397R1
TRMT10CCESCchr3101284448101284448GAMissense_Mutationp.E275K1
TRMT10CLUADchr3101283965101283965GAMissense_Mutationp.E114K1

check buttonCopy number variation (CNV) of TRMT10C
* Click on the image to open the original image in a new window.
all structure

check buttonFusion gene breakpoints (product of the structural variants (SVs)) across TRMT10C
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure


check button Fusion genes with this translation factor from FusionGDB2.0.
FusionGDB2 IDDiseaseSampleHgeneHchrHbpHstrandTgeneTchrTbpTstrand
45623SARCTCGA-DX-AB37-01ACNOT2chr1270713144+TRMT10Cchr3101283614+
45623BRCATCGA-AO-A03L-01ADHX35chr2037650578+TRMT10Cchr3101283614+
45623BRCATCGA-BH-A0HW-01AEPHA6chr396706837+TRMT10Cchr3101283614+
45623N/AAX381954FKBP5chr635618071-TRMT10Cchr3101285089-
45624N/AFN109904LIPAchr1091001255+TRMT10Cchr3101284306+


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Prognostic Analysis


check button Kaplan-Meier plots with logrank tests of overall survival (OS)
Cancer typeTranslation factorCoefficentHazard ratioWald test pvalLikelihool ratio pvalLogrank test pval# samples


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Translation factor and Gender


check button Differential gene expression between female and male. (Wilcoxon test, pval<0.05)
Cancer typeTranslation factorpvaladj.p

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Translation factor and Age


check button Differential gene expression between young and old age groups (Wilcoxon test, pval<0.05)
Cancer typeTranslation factorpvaladj.p

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Related Drugs


check button Drugs targeting genes involved in this translation factor.
(DrugBank Version 5.1.8 2021-05-08)
UniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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Related Diseases


check button Diseases associated with this translation factor.
(DisGeNet 4.0)
Disease IDDisease Name# PubMedsDisease source
C4310773COMBINED OXIDATIVE PHOSPHORYLATION DEFICIENCY 301CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT