TRUB1

protein-coding

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

Gene summary

Pseudouridine is an abundant component of rRNAs and tRNAs and is enzymatically generated by isomerization of uridine by pseudouridine synthase (Zucchini et al., 2003 [PubMed 12736709]).[supplied by OMIM, Mar 2008]

MANE transcript

NM_139169.5

Inheritance

—

ClinVar variants

U:42B:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.68

Max pathogenic AF

—

Genomic locus

chr10:114,938,195-114,977,676

External References & Databases

Ensembl (ENSG00000165832)

Transcript & Mutation Effects

hg38 • Region Span ~39.5 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to TRUB1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 41

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_139169.5. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar	1 clinvar		2
missense			40 clinvar	2 clinvar		42
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	42	3	0	45

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 16 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_139169.5	RefSeq	NP_631908.1	8	MANE Select
ENST00000298746.5	Ensembl	ENSP00000298746.3	8	MANE Select
ENST00000900221.1	Ensembl	ENSP00000570280.1	7	Standard
ENST00000900221.2	Ensembl	ENSP00000570280.1	7	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

tRNA modification
mRNA pseudouridine synthesis

Molecular Function

RNA binding
pseudouridine synthase activity

Cellular Component

nucleus
mitochondrion
cytosol

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000298746
Coding exons: 8
Length: 39479
Individuals with no LoFs: 125613
Homozygous LoFs: 0
Heterozygous LoFs: 135
Defined: 125748
p: 0.000537

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.502	163	182	0.895	0.00000867	2211
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00025	0.00025	rare
Latino/Admixed American	0.00044	0.00043	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00033	0.00033	rare
Finnish	0.0014	0.0014	notable
European (Non-Finnish)	0.00060	0.00060	rare
South Asian	0.00036	0.00036	rare
Other	0.00018	0.00016	rare

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.374

Gene Damage Prediction

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