GeneBe

TRUB2

TruB pseudouridine synthase family member 2, the group of Pseudouridine synthases

Basic information

Region (hg38): 9:128305159-128322447

Links

ENSG00000167112 ∙ NCBI:26995 ∙ OMIM:610727 ∙ HGNC:17170 ∙ Uniprot:O95900 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TRUB2 gene.

  • not_specified (62 variants)
  • not_provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TRUB2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000015679.3. 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
2
clinvar
 2
missense
60
clinvar
2
clinvar
 62
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 0 0 60 4 0
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
TRUB2protein_codingprotein_codingENST00000372890 813640
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
0.000003790.60612544803001257480.00119
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.04682092110.9910.00001302120
Missense in Polyphen6170.8040.86153698
Synonymous-0.87910291.31.120.00000591706
Loss of Function0.9061013.60.7356.60e-7163

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0009610.000948
Ashkenazi Jewish0.000.00
East Asian0.00005440.0000544
Finnish0.001200.00120
European (Non-Finnish)0.001990.00199
Middle Eastern0.00005440.0000544
South Asian0.0004250.000425
Other0.001300.00130

dbNSFP

Source: dbNSFP

Function
FUNCTION: Minor enzyme contributing to the isomerization of uridine to pseudouridine (pseudouridylation) of specific mitochondrial mRNAs (mt-mRNAs) such as COXI and COXIII mt-mRNAs (PubMed:27974379). As a component of a functional protein-RNA module, consisting of RCC1L, NGRN, RPUSD3, RPUSD4, TRUB2, FASTKD2 and 16S mitochondrial ribosomal RNA (16S mt-rRNA), controls 16S mt-rRNA abundance and is required for intra-mitochondrial translation (PubMed:27667664). {ECO:0000269|PubMed:27667664, ECO:0000269|PubMed:27974379}.;

Recessive Scores

pRec
0.0880

Intolerance Scores

loftool
0.836
rvis_EVS
0.44
rvis_percentile_EVS
77.91

Haploinsufficiency Scores

pHI
0.0810
hipred
N
hipred_score
0.376
ghis
0.474

Essentials

essential_gene_CRISPR
E
essential_gene_CRISPR2
E
essential_gene_gene_trap
E
gene_indispensability_pred
E
gene_indispensability_score
0.926

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Trub2
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);

Gene ontology

Biological process
pseudouridine synthesis;mRNA processing;positive regulation of mitochondrial translation
Cellular component
mitochondrial matrix;cytosol
Molecular function
RNA binding;protein binding;pseudouridine synthase activity