TSEN54 Gene

HGNC Family	tRNA-splicing endonuclease subunits (TSEN)
Name	TSEN54 tRNA splicing endonuclease subunit
Description	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]
Summary	{"type": "root", "children": [{"type": "p", "children": [{"type": "t", "text": "\nTSEN54 encodes a core subunit of the heterotetrameric tRNA splicing endonuclease complex that is essential for the proper removal of introns from precursor tRNAs—a critical step in RNA processing. Disruption of TSEN54 function, often by mutations, has been closely linked to early‐onset neurodegenerative conditions, notably several subtypes of pontocerebellar hypoplasia (PCH), such as PCH2 and PCH4. Studies have demonstrated that mutations in TSEN54, along with other TSEN subunits, impair the RNA splicing process and thereby contribute to severe cerebellar and pontine hypoplasia observed in affected individuals."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "1"}]}, {"type": "t", "text": ""}, {"type": "p", "children": [{"type": "t", "text": "\nExpanding on its clinical significance, TSEN54 mutations have been reported to cause not only PCH2—with marked cerebellar hemisphere involvement, progressive cerebral atrophy, microcephaly, and early childhood mortality—but also other PCH subtypes (including PCH4 and PCH5). Despite a shared pathological feature of defective neuronal development, the clinical and neuroimaging phenotypes can vary considerably, underscoring the genetic and mechanistic heterogeneity underlying these disorders. Not all cases of clinically defined PCH4 can be solely attributed to TSEN54 mutations, which indicates that additional genetic factors may influence disease manifestation."}, {"type": "fg", "children": [{"type": "fg_fs", "start_ref": "3", "end_ref": "5"}]}, {"type": "t", "text": ""}, {"type": "p", "children": [{"type": "t", "text": "\nMoreover, emerging research has identified novel TSEN54 variants that may be associated with atypical and later-onset forms of ataxia, diverging from the classic prenatal onset observed in conventional PCH presentations. In addition, while TSEN54’s role has been extensively studied in the realm of neurodevelopmental disorders, preliminary investigations now hint at its potential involvement in broader pathological contexts, such as hepatocellular carcinoma, although its exact function in malignancy remains to be elucidated."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "6"}]}]}]}]}, {"type": "rg", "children": [{"type": "r", "ref": 1, "children": [{"type": "t", "text": "Birgit S Budde, Yasmin Namavar, Peter G Barth, et al. "}, {"type": "b", "children": [{"type": "t", "text": "tRNA splicing endonuclease mutations cause pontocerebellar hypoplasia."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Nat Genet (2008)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1038/ng.204"}], "href": "https://doi.org/10.1038/ng.204"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "18711368"}], "href": "https://pubmed.ncbi.nlm.nih.gov/18711368"}]}, {"type": "r", "ref": 2, "children": [{"type": "t", "text": "D Cassandrini, R Biancheri, A Tessa, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Pontocerebellar hypoplasia: clinical, pathologic, and genetic studies."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Neurology (2010)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1212/WNL.0b013e3181f88173"}], "href": "https://doi.org/10.1212/WNL.0b013e3181f88173"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "20956791"}], "href": "https://pubmed.ncbi.nlm.nih.gov/20956791"}]}, {"type": "r", "ref": 3, "children": [{"type": "t", "text": "Stephen M Maricich, Kaashif A Aqeeb, Yalda Moayedi, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Pontocerebellar hypoplasia: review of classification and genetics, and exclusion of several genes known to be important for cerebellar development."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "J Child Neurol (2011)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1177/0883073810380047"}], "href": "https://doi.org/10.1177/0883073810380047"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "21383226"}], "href": "https://pubmed.ncbi.nlm.nih.gov/21383226"}]}, {"type": "r", "ref": 4, "children": [{"type": "t", "text": "Hülya Maraş-Genç, Emek Uyur-Yalçın, Rasim Özgür Rosti, et al. "}, {"type": "b", "children": [{"type": "t", "text": "TSEN54 gene-related pontocerebellar hypoplasia type 2 presenting with exaggerated startle response: report of two cases in a family."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Turk J Pediatr (2015)"}]}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "26701950"}], "href": "https://pubmed.ncbi.nlm.nih.gov/26701950"}]}, {"type": "r", "ref": 5, "children": [{"type": "t", "text": "Afrooz Sepahvand, Ehsan Razmara, Fatemeh Bitarafan, et al. "}, {"type": "b", "children": [{"type": "t", "text": "A homozygote variant in the tRNA splicing endonuclease subunit 54 causes pontocerebellar hypoplasia in a consanguineous Iranian family."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Mol Genet Genomic Med (2020)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1002/mgg3.1413"}], "href": "https://doi.org/10.1002/mgg3.1413"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "32697043"}], "href": "https://pubmed.ncbi.nlm.nih.gov/32697043"}]}, {"type": "r", "ref": 6, "children": [{"type": "t", "text": "Yi Qian, Haiyong Wang, Tao Jin, et al. "}, {"type": "b", "children": [{"type": "t", "text": "A familial late‑onset hereditary ataxia mimicking pontocerebellar hypoplasia caused by a novel TSEN54 mutation."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Mol Med Rep (2014)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.3892/mmr.2014.2342"}], "href": "https://doi.org/10.3892/mmr.2014.2342"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "24938831"}], "href": "https://pubmed.ncbi.nlm.nih.gov/24938831"}]}, {"type": "r", "ref": 7, "children": [{"type": "t", "text": "Bidong Fu, Minqin Zhou, Gelin Song, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Comprehensive analysis reveals TSEN54 as a robust prognosis biomarker and promising immune-related therapeutic target for hepatocellular carcinoma."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Aging (Albany NY) (2023)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.18632/aging.204645"}], "href": "https://doi.org/10.18632/aging.204645"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "37059591"}], "href": "https://pubmed.ncbi.nlm.nih.gov/37059591"}]}]}]}
Synonyms	SEN54L, PCH4, PCH5, PCH2A, SEN54
Proteins	SEN54_HUMAN
NCBI Gene ID	283989
API
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Predicted Functions
Co-expressed Genes
Expression in Tissues and Cell Lines

Functional Associations

TSEN54 has 5,413 functional associations with biological entities spanning 9 categories (molecular profile, organism, disease, phenotype or trait, functional term, phrase or reference, chemical, structural feature, cell line, cell type or tissue, gene, protein or microRNA, sequence feature) extracted from 110 datasets.

Click the + buttons to view associations for TSEN54 from the datasets below.

If available, associations are ranked by standardized value

Harmonizome 3.0

TSEN54 Gene

Functional Associations

Please acknowledge the Harmonizome in your publications by citing the following reference(s):

	Dataset	Summary
	Allen Brain Atlas Adult Human Brain Tissue Gene Expression Profiles	tissues with high or low expression of TSEN54 gene relative to other tissues from the Allen Brain Atlas Adult Human Brain Tissue Gene Expression Profiles dataset.
	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	tissues with high or low expression of TSEN54 gene relative to other tissues from the Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles dataset.
	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	tissue samples with high or low expression of TSEN54 gene relative to other tissue samples from the Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles dataset.
	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by Microarray	tissue samples with high or low expression of TSEN54 gene relative to other tissue samples from the Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by Microarray dataset.
	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq	tissue samples with high or low expression of TSEN54 gene relative to other tissue samples from the Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq dataset.
	Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles	tissues with high or low expression of TSEN54 gene relative to other tissues from the Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles dataset.
	BioGPS Mouse Cell Type and Tissue Gene Expression Profiles	cell types and tissues with high or low expression of TSEN54 gene relative to other cell types and tissues from the BioGPS Mouse Cell Type and Tissue Gene Expression Profiles dataset.
	CCLE Cell Line Gene CNV Profiles	cell lines with high or low copy number of TSEN54 gene relative to other cell lines from the CCLE Cell Line Gene CNV Profiles dataset.
	CCLE Cell Line Gene Expression Profiles	cell lines with high or low expression of TSEN54 gene relative to other cell lines from the CCLE Cell Line Gene Expression Profiles dataset.
	CCLE Cell Line Proteomics	Cell lines associated with TSEN54 protein from the CCLE Cell Line Proteomics dataset.
	CellMarker Gene-Cell Type Associations	cell types associated with TSEN54 gene from the CellMarker Gene-Cell Type Associations dataset.
	ChEA Transcription Factor Binding Site Profiles	transcription factor binding site profiles with transcription factor binding evidence at the promoter of TSEN54 gene from the CHEA Transcription Factor Binding Site Profiles dataset.
	ChEA Transcription Factor Targets	transcription factors binding the promoter of TSEN54 gene in low- or high-throughput transcription factor functional studies from the CHEA Transcription Factor Targets dataset.
	ChEA Transcription Factor Targets 2022	transcription factors binding the promoter of TSEN54 gene in low- or high-throughput transcription factor functional studies from the CHEA Transcription Factor Targets 2022 dataset.
	ClinVar Gene-Phenotype Associations	phenotypes associated with TSEN54 gene from the curated ClinVar Gene-Phenotype Associations dataset.
	ClinVar Gene-Phenotype Associations 2025	phenotypes associated with TSEN54 gene from the curated ClinVar Gene-Phenotype Associations 2025 dataset.
	CM4AI KOLF21J CRISPRi Gene Perturbation Atlas	gene perturbations changing expression of TSEN54 gene from the CM4AI KOLF21J CRISPRi Gene Perturbation Atlas dataset.
	CM4AI U2OS Cell Map Protein Localization Assemblies	assemblies containing TSEN54 protein from integrated AP-MS and IF data from the CM4AI U2OS Cell Map Protein Localization Assemblies dataset.
	COMPARTMENTS Curated Protein Localization Evidence Scores	cellular components containing TSEN54 protein from the COMPARTMENTS Curated Protein Localization Evidence Scores dataset.
	COMPARTMENTS Curated Protein Localization Evidence Scores 2025	cellular components containing TSEN54 protein from the COMPARTMENTS Curated Protein Localization Evidence Scores 2025 dataset.
	COMPARTMENTS Experimental Protein Localization Evidence Scores	cellular components containing TSEN54 protein in low- or high-throughput protein localization assays from the COMPARTMENTS Experimental Protein Localization Evidence Scores dataset.
	COMPARTMENTS Experimental Protein Localization Evidence Scores 2025	cellular components containing TSEN54 protein in low- or high-throughput protein localization assays from the COMPARTMENTS Experimental Protein Localization Evidence Scores 2025 dataset.
	COMPARTMENTS Text-mining Protein Localization Evidence Scores	cellular components co-occuring with TSEN54 protein in abstracts of biomedical publications from the COMPARTMENTS Text-mining Protein Localization Evidence Scores dataset.
	COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025	cellular components co-occuring with TSEN54 protein in abstracts of biomedical publications from the COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025 dataset.
	CORUM Protein Complexes	protein complexs containing TSEN54 protein from the CORUM Protein Complexes dataset.
	COSMIC Cell Line Gene CNV Profiles	cell lines with high or low copy number of TSEN54 gene relative to other cell lines from the COSMIC Cell Line Gene CNV Profiles dataset.
	COSMIC Cell Line Gene Mutation Profiles	cell lines with TSEN54 gene mutations from the COSMIC Cell Line Gene Mutation Profiles dataset.
	CTD Gene-Chemical Interactions	chemicals interacting with TSEN54 gene/protein from the curated CTD Gene-Chemical Interactions dataset.
	CTD Gene-Disease Associations	diseases associated with TSEN54 gene/protein from the curated CTD Gene-Disease Associations dataset.
	DISEASES Curated Gene-Disease Association Evidence Scores 2025	diseases involving TSEN54 gene from the DISEASES Curated Gene-Disease Association Evidence Scores 2025 dataset.
	DISEASES Experimental Gene-Disease Association Evidence Scores 2025	diseases associated with TSEN54 gene in GWAS datasets from the DISEASES Experimental Gene-Disease Assocation Evidence Scores 2025 dataset.
	DISEASES Text-mining Gene-Disease Association Evidence Scores	diseases co-occuring with TSEN54 gene in abstracts of biomedical publications from the DISEASES Text-mining Gene-Disease Assocation Evidence Scores dataset.
	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	diseases co-occuring with TSEN54 gene in abstracts of biomedical publications from the DISEASES Text-mining Gene-Disease Assocation Evidence Scores 2025 dataset.
	DisGeNET Gene-Disease Associations	diseases associated with TSEN54 gene in GWAS and other genetic association datasets from the DisGeNET Gene-Disease Associations dataset.
	DisGeNET Gene-Phenotype Associations	phenotypes associated with TSEN54 gene in GWAS and other genetic association datasets from the DisGeNET Gene-Phenoptype Associations dataset.
	ENCODE Histone Modification Site Profiles	histone modification site profiles with high histone modification abundance at TSEN54 gene from the ENCODE Histone Modification Site Profiles dataset.
	ENCODE Transcription Factor Binding Site Profiles	transcription factor binding site profiles with transcription factor binding evidence at the promoter of TSEN54 gene from the ENCODE Transcription Factor Binding Site Profiles dataset.
	ENCODE Transcription Factor Targets	transcription factors binding the promoter of TSEN54 gene in ChIP-seq datasets from the ENCODE Transcription Factor Targets dataset.
	ESCAPE Omics Signatures of Genes and Proteins for Stem Cells	PubMedIDs of publications reporting gene signatures containing TSEN54 from the ESCAPE Omics Signatures of Genes and Proteins for Stem Cells dataset.
	GeneRIF Biological Term Annotations	biological terms co-occuring with TSEN54 gene in literature-supported statements describing functions of genes from the GeneRIF Biological Term Annotations dataset.