TRMU

tRNA mitochondrial 2-thiouridylase

Basic information

Region (hg38): 22:46330875-46357340

Previous symbols: [ "TRMT" ]

Links

ENSG00000100416NCBI:55687OMIM:610230HGNC:25481Uniprot:O75648AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

  • acute infantile liver failure due to synthesis defect of mtDNA-encoded proteins (Supportive), mode of inheritance: AR
  • mitochondrial myopathy with reversible cytochrome C oxidase deficiency (Supportive), mode of inheritance: Mitochondrial
  • acute infantile liver failure due to synthesis defect of mtDNA-encoded proteins (Definitive), mode of inheritance: AR
  • acute infantile liver failure due to synthesis defect of mtDNA-encoded proteins (Strong), mode of inheritance: AR
  • Leigh syndrome (Moderate), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Deafness, aminoglycoside-induced; Liver failure, infantile, transient; Reversible infantile respiratory chain deficiencyAD/ARGastrointestinal; PharmacogenomicIndividuals with aminoglycoside-induced deafness may be at risk of deafness when treated with certain antibiotics; In Liver failure, infantile, transient, with supportive care, patients surviving the initial acute episode can recover and demonstrate typical development; Genetic diagnosis may be beneficial in order to determine therapyBiochemical; Gastrointestinal7689389; 11230176; 12408186; 16152638; 19732863; 21931168; 21931168
The inheritance of aminoglycoside-induced deafness may involve multiple, co-segregating variants

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TRMU gene.

  • not_provided (609 variants)
  • Acute_infantile_liver_failure_due_to_synthesis_defect_of_mtDNA-encoded_proteins (158 variants)
  • Aminoglycoside-induced_deafness (90 variants)
  • Inborn_genetic_diseases (63 variants)
  • not_specified (46 variants)
  • TRMU-related_disorder (45 variants)
  • EBV-positive_nodal_T-_and_NK-cell_lymphoma (1 variants)
  • Long_QT_syndrome (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TRMU gene is commonly pathogenic or not. These statistics are base on transcript: NM_000018006.5. Only rare variants are included in the table.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

EffectPLPVUSLBBSum
synonymous
8
clinvar
215
clinvar
5
clinvar
228
missense
4
clinvar
18
clinvar
140
clinvar
16
clinvar
5
clinvar
183
nonsense
13
clinvar
14
clinvar
27
start loss
1
2
3
frameshift
32
clinvar
48
clinvar
80
splice donor/acceptor (+/-2bp)
2
clinvar
35
clinvar
2
clinvar
39
Total 52 117 150 231 10

Highest pathogenic variant AF is 0.00020631842

Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
TRMUprotein_codingprotein_codingENST00000290846 1126466
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
1.53e-160.003351256680801257480.000318
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-0.3322472331.060.00001292766
Missense in Polyphen9097.8550.919731185
Synonymous-3.1513192.51.420.00000546802
Loss of Function-0.4392320.81.109.74e-7241

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0008410.000839
Ashkenazi Jewish0.000.00
East Asian0.0002720.000272
Finnish0.000.00
European (Non-Finnish)0.0003080.000308
Middle Eastern0.0002720.000272
South Asian0.0006530.000653
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: Catalyzes the 2-thiolation of uridine at the wobble position (U34) of mitochondrial tRNA(Lys), tRNA(Glu) and tRNA(Gln). Required for the formation of 5-taurinomethyl-2- thiouridine (tm5s2U) of mitochondrial tRNA(Lys), tRNA(Glu), and tRNA(Gln) at the wobble position. ATP is required to activate the C2 atom of the wobble base. {ECO:0000269|PubMed:15509579, ECO:0000269|PubMed:15944150, ECO:0000269|PubMed:16826519}.;
Disease
DISEASE: Liver failure, infantile, transient (LFIT) [MIM:613070]: A transient disorder of hepatic function characterized by elevated liver enzymes, jaundice, vomiting, coagulopathy, hyperbilirubinemia, increased serum lactate. Patients who survive the initial acute episode can recover, show normal development and have no recurrence. {ECO:0000269|PubMed:19732863}. Note=The disease is caused by mutations affecting the gene represented in this entry.;

Recessive Scores

pRec
0.234

Intolerance Scores

loftool
0.835
rvis_EVS
-0.07
rvis_percentile_EVS
48.69

Haploinsufficiency Scores

pHI
0.198
hipred
N
hipred_score
0.197
ghis
0.506

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
S
essential_gene_gene_trap
N
gene_indispensability_pred
N
gene_indispensability_score
0.230

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Trmu
Phenotype
cellular phenotype; homeostasis/metabolism phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); liver/biliary system phenotype; immune system phenotype;

Gene ontology

Biological process
tRNA wobble position uridine thiolation
Cellular component
nucleoplasm;mitochondrion
Molecular function
tRNA binding;ATP binding;sulfurtransferase activity