TRUB1

TruB pseudouridine synthase family member 1, the group of Pseudouridine synthases

Basic information

Region (hg38): 10:114938195-114977676

Links

ENSG00000165832 ∙ NCBI:142940 ∙ OMIM:610726 ∙ HGNC:16060 ∙ Uniprot:Q8WWH5 ∙ 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 TRUB1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TRUB1 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				1		1
missense			11	1		12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	11	2	0

Variants in TRUB1

This is a list of pathogenic ClinVar variants found in the TRUB1 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-114938278-G-A		not specified	Likely benign (Nov 08, 2022)
10-114938280-G-A			Likely benign (Jun 01, 2020)
10-114938320-G-C		not specified	Uncertain significance (Jan 02, 2024)
10-114938426-A-C		not specified	Uncertain significance (May 10, 2024)
10-114938474-T-A		not specified	Uncertain significance (May 24, 2024)
10-114938478-C-G		not specified	Uncertain significance (Apr 23, 2024)
10-114942681-A-G		not specified	Uncertain significance (May 11, 2022)
10-114942725-G-A		not specified	Uncertain significance (Aug 16, 2021)
10-114951130-G-A		not specified	Uncertain significance (Apr 08, 2024)
10-114970434-C-T		not specified	Uncertain significance (Sep 22, 2023)
10-114972184-A-G		not specified	Uncertain significance (Feb 17, 2024)
10-114972233-G-A		not specified	Uncertain significance (Nov 22, 2022)
10-114972239-C-G		not specified	Uncertain significance (Mar 23, 2022)
10-114975141-A-G		not specified	Uncertain significance (Feb 15, 2023)
10-114975209-A-G		not specified	Uncertain significance (Jan 09, 2023)
10-114975243-A-G		not specified	Uncertain significance (Jul 14, 2021)
10-114975300-C-G		not specified	Uncertain significance (Jan 04, 2024)
10-114975320-T-A		not specified	Uncertain significance (Apr 23, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TRUB1	protein_coding	protein_coding	ENST00000298746	8	39479

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000233	0.740	125613	0	135	125748	0.000537

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.502	163	182	0.895	0.00000867	2211
Missense in Polyphen		33	42.159	0.78275		499
Synonymous	-0.305	76	72.7	1.05	0.00000365	735
Loss of Function	1.19	11	16.2	0.680	8.55e-7	203

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000683	0.000682
Ashkenazi Jewish	0.00	0.00
East Asian	0.000327	0.000326
Finnish	0.00139	0.00139
European (Non-Finnish)	0.000601	0.000598
Middle Eastern	0.000327	0.000326
South Asian	0.000360	0.000359
Other	0.000175	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Pseudouridine synthase that catalyzes pseudouridylation of mRNAs (PubMed:28073919). Mediates pseudouridylation of mRNAs with the consensus sequence 5'-GUUCNANNC-3', harboring a stem-loop structure (PubMed:28073919). Constitutes the major pseudouridine synthase acting on mRNAs (PubMed:28073919). {ECO:0000269|PubMed:28073919}.

Recessive Scores

• pRec: 0.200

Intolerance Scores

• loftool: 0.803
• rvis_EVS: 0.08
• rvis_percentile_EVS: 60.31

Haploinsufficiency Scores

• pHI: 0.144
• hipred: N
• hipred_score: 0.387
• ghis: 0.594

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.374

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Trub1

Gene ontology

• Biological process: tRNA modification;mRNA pseudouridine synthesis
• Cellular component: nucleus;mitochondrion;cytosol
• Molecular function: RNA binding;pseudouridine synthase activity