TSEN54
tRNA splicing endonuclease subunit 54
Gene Information Card
| Symbol | TSEN54 |
|---|---|
| Full Name | tRNA splicing endonuclease subunit 54 |
| Gene Type | protein-coding |
| Chromosomal Location | 17q25.1 |
| NCBI Gene ID | 283989 ncbi.nlm.nih.gov/gene/283989 |
| Ensembl ID | ENSG00000108379 |
| UniProt ID | Q7Z6J9 |
| OMIM ID | 608755 |
| HGNC ID | 27561 |
| Aliases | SEN54, PCH2A, PCH4, PCH5 |
Description
TSEN54 encodes the 54 kDa subunit of the tRNA splicing endonuclease complex, which is essential for the removal of introns from pre-tRNA molecules. Mutations in this gene are associated with pontocerebellar hypoplasia types 2, 4, and 5, a group of severe neurodegenerative disorders characterized by impaired brain development.
Disease Associations
| Disease category | Pathophysiological mechanism | Genomic evidence |
|---|---|---|
| Pontocerebellar hypoplasia type 2 (PCH2) | Loss-of-function mutations impair tRNA splicing, leading to defective neuronal development and degeneration. | ClinVar, OMIM |
| Pontocerebellar hypoplasia type 4 (PCH4) | Severe loss of TSEN54 function disrupts tRNA maturation, causing early-onset encephalopathy and cerebellar atrophy. | ClinVar, OMIM |
| Pontocerebellar hypoplasia type 5 (PCH5) | Mutations result in complete loss of tRNA endonuclease activity, leading to prenatal onset of microcephaly and brainstem hypoplasia. | ClinVar, OMIM |
Expression Profile
Tissue Expression
| Tissue | nTPM | level |
|---|---|---|
| Cerebellum | 8.2 | Low |
| Cerebral cortex | 6.5 | Low |
| Heart | 4.1 | Low |
| Liver | 3.8 | Low |
| Testis | 2.9 | Low |
Cell Line Expression
| Cell Line | nTPM | Notes |
|---|---|---|
| HEK293 | 5.1 | Embryonic kidney cells |
| SH-SY5Y | 4.3 | Neuroblastoma cells |
| HeLa | 3.7 | Cervical carcinoma cells |
Data source：Human Protein Atlas（proteinatlas.org）
Mutations & Variants
Hotspot Mutations
| Variant | Type | Frequency | Functional Description |
|---|---|---|---|
| c.919G>T (p.Ala307Ser) | Missense | Common in PCH2 | Reduced tRNA splicing activity |
| c.1267C>T (p.Arg423Trp) | Missense | Rare | Impaired complex assembly |
| c.2T>C (p.Met1Thr) | Start loss | Very rare | Complete loss of protein |
Mutation functional classification
Loss of Function (LOF)
Most TSEN54 mutations lead to loss of tRNA splicing endonuclease activity, causing pontocerebellar hypoplasia.
Gain of Function (GOF)
No evidence of gain-of-function mutations.
Dominant Negative (DN)
Not reported; all pathogenic mutations are recessive.
View complete mutation data：
Gene Ontology (GO)
| • tRNA splicing | • via endonucleolytic cleavage and ligation |
| • tRNA-type intron endonuclease activity | • nucleus |
| • cytoplasm |
Pathways
• tRNA splicing
• RNA processing
Protein Summary
TSEN54 is a 54 kDa protein that forms part of the tRNA splicing endonuclease complex. It is required for the excision of introns from pre-tRNA molecules, a critical step in tRNA maturation. The protein localizes to the nucleus and cytoplasm and is expressed ubiquitously, with highest levels in neural tissues.
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