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.

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.

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				2		2
missense			29	1		30
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	29	3	0

Variants in TRUB2

This is a list of pathogenic ClinVar variants found in the TRUB2 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
9-128309560-G-A		not specified	Uncertain significance (Jan 12, 2024)
9-128309590-G-A		not specified	Uncertain significance (Aug 20, 2024)
9-128309600-A-T		not specified	Uncertain significance (Aug 23, 2021)
9-128309617-G-A		not specified	Uncertain significance (Jul 19, 2023)
9-128309643-C-T			Benign/Likely benign (Sep 01, 2022)
9-128309663-C-G		not specified	Uncertain significance (Jan 23, 2024)
9-128309687-T-C		not specified	Likely benign (Feb 28, 2024)
9-128309695-C-A		not specified	Uncertain significance (Nov 15, 2024)
9-128309728-T-A		not specified	Uncertain significance (Apr 18, 2023)
9-128309765-C-T		not specified	Uncertain significance (Jan 04, 2024)
9-128309770-C-T		not specified	Uncertain significance (Sep 30, 2024)
9-128309773-G-A		not specified	Uncertain significance (Dec 17, 2023)
9-128309779-C-T		not specified	Uncertain significance (Sep 17, 2021)
9-128309827-T-C		not specified	Uncertain significance (Dec 19, 2022)
9-128309827-T-G		not specified	Uncertain significance (Nov 10, 2022)
9-128309840-G-A		not specified	Uncertain significance (Oct 26, 2022)
9-128310922-C-T		not specified	Uncertain significance (Dec 18, 2023)
9-128310950-T-C		not specified	Uncertain significance (Aug 22, 2023)
9-128310956-T-A		not specified	Uncertain significance (Apr 19, 2024)
9-128310961-C-T		not specified	Uncertain significance (Mar 27, 2023)
9-128310962-G-A		not specified	Uncertain significance (May 27, 2022)
9-128311539-C-A		not specified	Uncertain significance (Nov 10, 2024)
9-128311563-C-A		not specified	Uncertain significance (Dec 04, 2024)
9-128311565-G-A		not specified	Uncertain significance (Feb 27, 2023)
9-128311596-C-T		not specified	Uncertain significance (Jul 30, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TRUB2	protein_coding	protein_coding	ENST00000372890	8	13640

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000379	0.606	125448	0	300	125748	0.00119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0468	209	211	0.991	0.0000130	2120
Missense in Polyphen		61	70.804	0.86153		698
Synonymous	-0.879	102	91.3	1.12	0.00000591	706
Loss of Function	0.906	10	13.6	0.735	6.60e-7	163

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000961	0.000948
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00120	0.00120
European (Non-Finnish)	0.00199	0.00199
Middle Eastern	0.0000544	0.0000544
South Asian	0.000425	0.000425
Other	0.00130	0.00130

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

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

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