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10 sources retrieved Β· Most recent: April 2026 Β· Index updated 14 days ago
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TSEN2
tRNA splicing endonuclease subunit 2
Chromosome 3 Β· 3p25.2
NCBI Gene: 80746Ensembl: ENSG00000154743.19HGNC: HGNC:28422UniProt: A0A7P0T8F8
37PubMed Papers
21Diseases
0Drugs
25Pathogenic Variants
CLINICAL
OMIM Disease Gene
DATA QUALITY
βœ“ Experimental GO Evidenceβœ“ Swiss-Prot Reviewed
tRNA splicing, via endonucleolytic cleavage and ligationnucleoplasmprotein bindingtRNA-type intron splice site recognition and cleavagepontocerebellar hypoplasia type 2Bpontocerebellar hypoplasiaNon-syndromic pontocerebellar hypoplasianeurodegenerative disease
✦AI Summary

TSEN2 constitutes one of the two catalytic subunits of the tRNA splicing endonuclease (TSEN) complex, which is responsible for removing introns from precursor tRNAs (pre-tRNAs) 12. The human TSEN complex comprises four subunits (TSEN2, TSEN15, TSEN34, and TSEN54) that collectively recognize and cleave pre-tRNA at both 5' and 3' splice sites 1. TSEN2 specifically carries the active site for 5'-splice site cleavage, working in coordination with TSEN54 for 3'-splice site cleavage 2. Structural studies reveal that TSEN2, along with TSEN34 and TSEN54, recognizes the mature domain of pre-tRNA through conserved structural elements, positioning the anticodon stem to place splice sites into their respective catalytic centers 1. The complex employs a molecular ruler mechanism where the mature tRNA body is recognized while intron sequences make no direct contact with TSEN, allowing accommodation of varying intron lengths 1. Disease relevance is significant, as biallelic pathogenic variants in TSEN2 cause pontocerebellar hypoplasia type 2B (PCH2B), characterized by cerebellar hypoplasia, progressive microcephaly, developmental delay, and seizures 34. Additionally, specific TSEN2 mutations have been associated with atypical hemolytic uremic syndrome, suggesting a connection between tRNA biology and vascular endothelium homeostasis 5.

Sources cited
1
TSEN2 is one of four subunits in human TSEN complex and structural basis of pre-tRNA recognition
PMID: 37028420
2
TSEN2 carries 5'-splice site cleavage activity and cooperative recognition of pre-tRNA mature body
PMID: 37770519
3
TSEN2 mutations cause pontocerebellar hypoplasia type 2B with characteristic clinical features
PMID: 23562994
4
Biallelic TSEN2 variants cause PCH2 with progressive microcephaly and cerebellar atrophy
PMID: 40858833
5
TSEN2 splice site mutations associated with atypical hemolytic uremic syndrome and TRACK syndrome
PMID: 34964109
Disease Associationsβ“˜21
pontocerebellar hypoplasia type 2BOpen Targets
0.74Strong
pontocerebellar hypoplasiaOpen Targets
0.68Moderate
Non-syndromic pontocerebellar hypoplasiaOpen Targets
0.52Moderate
neurodegenerative diseaseOpen Targets
0.50Moderate
genetic disorderOpen Targets
0.41Moderate
pontocerebellar hypoplasia type 2Open Targets
0.37Weak
metabolic diseaseOpen Targets
0.35Weak
hemolytic-uremic syndromeOpen Targets
0.33Weak
type 2 diabetes mellitusOpen Targets
0.29Weak
Alzheimer diseaseOpen Targets
0.28Weak
respiratory tract infectious disorderOpen Targets
0.28Weak
benign digestive system neoplasmOpen Targets
0.24Weak
HypercholesterolemiaOpen Targets
0.24Weak
lower urinary tract calculusOpen Targets
0.23Weak
coronary artery diseaseOpen Targets
0.22Weak
systemic lupus erythematosusOpen Targets
0.21Weak
diabetes mellitusOpen Targets
0.16Weak
congenital contractures of the limbs and face, hypotonia, and developmental delayOpen Targets
0.12Weak
metabolic syndromeOpen Targets
0.11Weak
smoking behaviorOpen Targets
0.09Suggestive
Pontocerebellar hypoplasia 2BUniProt
Pathogenic Variants25
NM_025265.4(TSEN2):c.958A>T (p.Lys320Ter)Pathogenic
Pontoneocerebellar hypoplasia|Pontocerebellar hypoplasia type 2B|not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 320
NM_025265.4(TSEN2):c.917del (p.Phe306fs)Pathogenic
not provided|Pontoneocerebellar hypoplasia
β˜…β˜…β˜†β˜†2025β†’ Residue 306
NM_025265.4(TSEN2):c.1099+1G>ALikely pathogenic
not provided|Pontoneocerebellar hypoplasia
β˜…β˜…β˜†β˜†2025
NM_025265.4(TSEN2):c.57C>A (p.Tyr19Ter)Pathogenic
Pontoneocerebellar hypoplasia|Pontocerebellar hypoplasia type 2B
β˜…β˜…β˜†β˜†2024β†’ Residue 19
NM_025265.4(TSEN2):c.353_354del (p.Gln118fs)Likely pathogenic
Pontocerebellar hypoplasia type 2B|Pontoneocerebellar hypoplasia
β˜…β˜…β˜†β˜†2024β†’ Residue 118
NM_025265.4(TSEN2):c.960+1_960+5delLikely pathogenic
Pontocerebellar hypoplasia type 2B|Pontoneocerebellar hypoplasia
β˜…β˜…β˜†β˜†2024
NM_025265.4(TSEN2):c.1260_1264del (p.Cys421fs)Likely pathogenic
Pontocerebellar hypoplasia type 2B
β˜…β˜†β˜†β˜†2026β†’ Residue 421
NM_025265.4(TSEN2):c.583G>T (p.Glu195Ter)Pathogenic
not provided
β˜…β˜†β˜†β˜†2026β†’ Residue 195
NM_025265.4(TSEN2):c.190-2A>GLikely pathogenic
not provided
β˜…β˜†β˜†β˜†2025
NM_025265.4(TSEN2):c.790del (p.Glu264fs)Pathogenic
not provided
β˜…β˜†β˜†β˜†2025β†’ Residue 264
NM_025265.4(TSEN2):c.1100-2A>CLikely pathogenic
not provided
β˜…β˜†β˜†β˜†2025
NM_025265.4(TSEN2):c.1016del (p.Phe339fs)Pathogenic
not provided
β˜…β˜†β˜†β˜†2025β†’ Residue 339
NM_025265.4(TSEN2):c.1100-5T>ALikely pathogenic
Hemolytic-uremic syndrome|not provided
β˜…β˜†β˜†β˜†2024
NM_025265.4(TSEN2):c.695_699del (p.Arg232fs)Likely pathogenic
Pontocerebellar hypoplasia type 2B
β˜…β˜†β˜†β˜†2024β†’ Residue 232
NM_025265.4(TSEN2):c.580C>T (p.Gln194Ter)Likely pathogenic
Pontocerebellar hypoplasia type 2B
β˜…β˜†β˜†β˜†2024β†’ Residue 194
NM_025265.4(TSEN2):c.1048C>T (p.Arg350Ter)Likely pathogenic
Pontocerebellar hypoplasia type 2B
β˜…β˜†β˜†β˜†2024β†’ Residue 350
NM_025265.4(TSEN2):c.200del (p.Gly67fs)Likely pathogenic
Pontocerebellar hypoplasia type 2B
β˜…β˜†β˜†β˜†2024β†’ Residue 67
NM_025265.4(TSEN2):c.215C>A (p.Ser72Ter)Pathogenic
Inborn genetic diseases
β˜…β˜†β˜†β˜†2021β†’ Residue 72
NM_025265.4(TSEN2):c.770_776delinsCA (p.Tyr257fs)Pathogenic
Pontocerebellar hypoplasia type 2B
β˜…β˜†β˜†β˜†2018β†’ Residue 257
NM_025265.4(TSEN2):c.1037A>G (p.Tyr346Cys)Likely pathogenic
Pontocerebellar hypoplasia type 2B
β˜…β˜†β˜†β˜†2018β†’ Residue 346
View on ClinVar β†—
Related Genes
TRIP10Protein interaction82%CSTF2Protein interaction81%CPSF4Protein interaction81%CPSF6Protein interaction81%CPSF1Protein interaction81%TSEN34Protein interaction79%
Tissue Expression6 tissues
Ovary
100%
Heart
82%
Liver
69%
Lung
50%
Brain
50%
Bone Marrow
38%
Gene Interaction Network
Click a node to explore
TSEN2TRIP10CSTF2CPSF4CPSF6CPSF1TSEN34
PROTEIN STRUCTURE
Preparing viewer…
PDB8HMZ Β· 2.90 Γ… Β· EM
View on RCSB β†—
Constraintβ“˜
LOEUFβ“˜
1.21LoF Tolerant
pLIβ“˜
0.00Tolerant
Observed/Expected LoF0.96 [0.76–1.21]
RankingsWhere TSEN2 stands among ~20K protein-coding genes
  • #10,717of 20,598
    Most Researched37
  • #1,990of 5,498
    Most Pathogenic Variants25
  • #12,745of 17,882
    Most Constrained (LOEUF)1.21
Genes detectedTSEN2
Sources retrieved10 papers
Response timeβ€”
πŸ“„ Sources
10β–Ό
1
Management of pediatric hemolytic uremic syndrome.
PMID: 38523374
Turk J Pediatr Β· 2024
1.00
2
Pontocerebellar hypoplasia type 2 and TSEN2: review of the literature and two novel mutations.
PMID: 23562994
Eur J Med Genet Β· 2013
0.90
3
Structural basis of pre-tRNA intron removal by human tRNA splicing endonuclease.
PMID: 37028420
Mol Cell Β· 2023
0.80
4
Cotranscription and intergenic splicing of the PPARG and TSEN2 genes in cattle.
PMID: 16595010
BMC Genomics Β· 2006
0.70
5
[Pontocerebellar hypoplasia type 2B due to compound heterozygous variants of TSEN2 gene: A case report and literature review].
PMID: 41621844
Zhonghua Yi Xue Yi Chuan Xue Za Zhi Β· 2026
0.60