TSEN54 tRNA splicing endonuclease subunit 54 [Homo sapiens (human)] - Gene

Summary

Official Symbol: TSEN54provided by HGNC
Official Full Name: tRNA splicing endonuclease subunit 54provided by HGNC
Primary source: HGNC:HGNC:27561
See related: Ensembl:ENSG00000182173 MIM:608755; AllianceGenome:HGNC:27561
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: PCH4; PCH5; PCH2A; sen54; SEN54L
Summary: This gene encodes a subunit of the tRNA splicing endonuclease complex, which catalyzes the removal of introns from precursor tRNAs. The complex is also implicated in pre-mRNA 3-prime end processing. Mutations in this gene result in pontocerebellar hypoplasia type 2.[provided by RefSeq, Oct 2009]
Expression: Ubiquitous expression in spleen (RPKM 8.3), duodenum (RPKM 7.0) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 17q25.1

Exon count:: 11

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	17	NC_000017.11 (75516528..75524735)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	17	NC_060941.1 (76409894..76418101)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	17	NC_000017.10 (73512609..73520816)

Chromosome 17 - NC_000017.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Comprehensive analysis reveals TSEN54 as a robust prognosis biomarker and promising immune-related therapeutic target for hepatocellular carcinoma.
Title: Comprehensive analysis reveals TSEN54 as a robust prognosis biomarker and promising immune-related therapeutic target for hepatocellular carcinoma.
A homozygote variant in the tRNA splicing endonuclease subunit 54 causes pontocerebellar hypoplasia in a consanguineous Iranian family.
Title: A homozygote variant in the tRNA splicing endonuclease subunit 54 causes pontocerebellar hypoplasia in a consanguineous Iranian family.
TSEN54 gene-related pontocerebellar hypoplasia type 2 presented with exaggerated startle response in cousins.
Title: TSEN54 gene-related pontocerebellar hypoplasia type 2 presenting with exaggerated startle response: report of two cases in a family.
A novel heterozygous mutation was found in the TSEN54 gene by c.254A > T(+) (p.E85V), which may be a new subtype of hereditary ataxia
Title: A familial late‑onset hereditary ataxia mimicking pontocerebellar hypoplasia caused by a novel TSEN54 mutation.
TSEN54 mutation causes a severe form of pontocerebellar hypoplasia type 1 in a family.
Title: TSEN54 mutation in a child with pontocerebellar hypoplasia type 1.
The results demonistrated that not all cases of clinically defined pontocerebellar hypoplasia-4 result from mutations in TSEN54.
Title: Pontocerebellar hypoplasia: review of classification and genetics, and exclusion of several genes known to be important for cerebellar development.
We confirm that the common p.A307S mutation in TSEN54 is responsible for most of the patients with a PCH2 phenotype.
Title: Pontocerebellar hypoplasia: clinical, pathologic, and genetic studies.
In two subtypes, PCH2 and PCH4, we identified mutations in three of the four different subunits of the tRNA-splicing endonuclease complex.
Title: tRNA splicing endonuclease mutations cause pontocerebellar hypoplasia.

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Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Pontocerebellar hypoplasia type 2A MedGen: C1848526 OMIM: 277470 GeneReviews: TSEN54 Pontocerebellar Hypoplasia	not available
Pontocerebellar hypoplasia type 4 MedGen: C1856974 OMIM: 225753 GeneReviews: TSEN54 Pontocerebellar Hypoplasia	not available
Pontocerebellar hypoplasia type 5 MedGen: C1857762 OMIM: 610204 GeneReviews: TSEN54 Pontocerebellar Hypoplasia	not available

Variation

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See Variation Viewer (GRCh37.p13)

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in mRNA processing	IEA Inferred from Electronic Annotation more info
involved_in tRNA splicing, via endonucleolytic cleavage and ligation	IDA Inferred from Direct Assay more info	PubMed
involved_in tRNA-type intron splice site recognition and cleavage	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
located_in nucleolus	IEA Inferred from Electronic Annotation more info
located_in nucleoplasm	TAS Traceable Author Statement more info
part_of tRNA-intron endonuclease complex	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: tRNA-splicing endonuclease subunit Sen54

Names: SEN54 homolog; TSEN54 tRNA splicing endonuclease subunit; hsSen54; tRNA-intron endonuclease Sen54

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.