TSEN54

Chr 17AR

tRNA splicing endonuclease subunit 54

Also known as: PCH2A, PCH4, PCH5, SEN54L, sen54

NCBI Gene: 283989ENSG00000182173UniProt: Q7Z6J9OMIM: 608755

This gene encodes a subunit of the tRNA splicing endonuclease complex that catalyzes intron removal from precursor tRNAs and is involved in pre-mRNA 3-prime end processing. Mutations cause pontocerebellar hypoplasia types 2A, 4, and 5 through autosomal recessive inheritance. The pathogenic mechanism involves disrupted tRNA processing leading to defective protein synthesis.

OMIMResearchSummary from RefSeq, OMIM, UniProt
LOFmechanismARLOEUF 0.883 OMIM phenotypes
Clinical Summary— TSEN54
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
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Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint
0.88LOEUF
pLI 0.000
Z-score 2.03
OE 0.57 (0.38–0.88)
Tolerant

Typical tolerance to LoF variation

Missense Constraint
-0.07Z-score
OE missense 1.01 (0.92–1.11)
299 obs / 295.4 exp
Tolerant

Tolerant to missense variation

Observed / Expected Ratios
LoF OE0.57 (0.38–0.88)
0≤0.351.4
Missense OE1.01 (0.92–1.11)
0≤0.61.4
Synonymous OE1.09
0≤1.21.6
LoF obs/exp: 15 / 26.2Missense obs/exp: 299 / 295.4Syn Z: -0.76

ClinVar Variant Classifications

0 submitted variants in ClinVar

ClinVar

Protein Context — Lollipop Plot

TSEN54 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

3D Protein StructureAlphaFold

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

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Clinical Literature
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Full-Text Mentions
NLP-detected gene mentions in article bodies · via PubTator3
PubTator3
Top 5 full-text resultsSearch PubTator3 ↗
Key Publications
Landmark & review papers · by relevance
PubMed
Refining the mutational spectrum and gene-phenotype correlates in pontocerebellar hypoplasia: results of a multicentric study.
Nuovo S et al.·J Med Genet
2022
Exome Sequencing of Consanguineous Pashtun Families With Familial Epilepsy Reveals Causative and Candidate Variants in TSEN54, MOCS2, and OPHN1.
Khan A et al.·Clin Genet
2025
Broadening the phenotype and genotype spectrum of novel mutations in pontocerebellar hypoplasia with a comprehensive molecular literature review.
Ghasemi MR et al.·BMC Med Genomics
2024Review
TSEN54 missense variant in Standard Schnauzers with leukodystrophy.
Störk T et al.·PLoS Genet
2019
A homozygote variant in the tRNA splicing endonuclease subunit 54 causes pontocerebellar hypoplasia in a consanguineous Iranian family.
Sepahvand A et al.·Mol Genet Genomic Med
2020Case report
Top 5 results · since 2015Search PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗

External Resources

Links to major genomics databases and tools

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients