Seroatlas · Human Serome Atlas

TSEN54

tRNA-splicing endonuclease subunit Sen54

Also known as: SEN54, SEN54_HUMAN, SEN54L

Cross-references: UniProt · Ensembl · Human Protein Atlas · GeneCards · NCBI Gene

Protein identityUniProt · HPA

UniProt accession
Q7Z6J9
Gene
TSEN54
Ensembl
ENSG00000182173
Chromosome
17
Canonical length
526 aa
Protein class
Disease related genes, Human disease related genes, Predicted intracellular proteins
Subcellular location
Nucleoplasm

OverviewNCBI Gene

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]

Canonical amino-acid sequenceUniProt

526 residues, UniProt reviewed canonical sequence.

>Q7Z6J9|TSEN54
     1  MEPEPEPAAV EVPAGRVLSA RELFAARSRS QKLPQRSHGP KDFLPDGSAA QAERLRRCRE
    61  ELWQLLAEQR VERLGSLVAA EWRPEEGFVE LKSPAGKFWQ TMGFSEQGRQ RLHPEEALYL
   121  LECGSIHLFH QDLPLSIQEA YQLLLTDHTV TFLQYQVFSH LKRLGYVVRR FQPSSVLSPY
   181  ERQLNLDASV QHLEDGDGKR KRSSSSPRSI NKKAKALDNS LQPKSLAASS PPPCSQPSQC
   241  PEEKPQESSP MKGPGGPFQL LGSLGPSPGP AREGVGCSWE SGRAENGVTG AGKRRWNFEQ
   301  ISFPNMASDS RHTLLRAPAP ELLPANVAGR ETDAESWCQK LNQRKEKLSR REREHHAEAA
   361  QFQEDVNADP EVQRCSSWRE YKELLQRRQV QRSQRRAPHL WGQPVTPLLS PGQASSPAVV
   421  LQHISVLQTT HLPDGGARLL EKSGGLEIIF DVYQADAVAT FRKNNPGKPY ARMCISGFDE
   481  PVPDLCSLKR LSYQSGDVPL IFALVDHGDI SFYSFRDFTL PQDVGH

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against TSEN54 can act on the native protein depends on physical access: surface and secreted proteins are reachable by circulating antibodies, intracellular proteins usually are not.

Antibody reachability
Intracellular
Secreted
No
Transmembrane segments
0
Mean surface accessibility (rSASA)
0.48
Highest tissue expression
11 nTPM

Expression across tissuesHPA

Tissue

  • skin: 11 nTPM
  • spleen: 9.4 nTPM
  • pancreas: 9.3 nTPM
  • spinal cord: 8.2 nTPM
  • esophagus: 7.5 nTPM
  • stomach: 7.5 nTPM

Single-cell type

  • mast cells: 103 nCPM
  • differentiating spermatogonia: 90 nCPM
  • nk-cells: 82 nCPM
  • t-cells: 77 nCPM
  • innate lymphoid cells: 62 nCPM
  • retinal horizontal cells: 58 nCPM

Immune cell

  • gdT-cell: 82 nTPM
  • memory CD8 T-cell: 63 nTPM
  • MAIT T-cell: 56 nTPM
  • naive CD8 T-cell: 50 nTPM
  • NK-cell: 48 nTPM
  • memory CD4 T-cell: 34 nTPM

Brain region

  • cerebellum: 7.5 nTPM
  • medulla oblongata: 7.5 nTPM
  • white matter: 6.6 nTPM
  • basal ganglia: 5.6 nTPM
  • spinal cord: 5.5 nTPM
  • midbrain: 5.3 nTPM

DiseaseUniProt · ClinVar · IEDB · PubMed

Four sources answering four different questions about TSEN54.

Disease | AllUniProt

Conditions TSEN54 is implicated in, by any mechanism.

Disease | GeneticClinVar

83 pathogenic / likely-pathogenic of 726 ClinVar records.

Conditions with pathogenic or likely-pathogenic variants.

  • Pontocerebellar hypoplasia type 4
  • Pontocerebellar hypoplasia type 2A
  • Pontocerebellar hypoplasia type 5
  • Pontoneocerebellar hypoplasia
  • Olivopontocerebellar hypoplasia

Genetic constraint and essentialitygnomAD · DepMap

Does the body need this protein intact? Low LOEUF or a strong DepMap dependency means loss or blockade of the protein is likely to be felt.

gnomAD LOEUF (loss-of-function intolerance)
0.88
gnomAD pLI
0
gnomAD missense Z
-0.07
DepMap mean gene effect
-0.83
DepMap dependency class
common

Cancer expressionTCGA

Across TCGA tumor cohorts, this protein is over-expressed in roughly 9% of surveyed tumor types (aggregate summary; per-cohort expression, alteration, and survival load in the interactive view).

OntologyGO

Biological processes

Cellular components

Protein domainsUniProt · Pfam · InterPro

  • tRNA-splicing endonuclease, subunit Sen54, N-terminal
  • tRNA-splicing endonuclease, subunit Sen54
  • tRNA-splicing endonuclease subunit sen54 N-term

KeywordsUniProt

InteractionsUniProt · HPA

Protein binding partners of TSEN54 in the human serome: UniProt-annotated complex subunits plus reported interactors. Each links to its own Seroatlas record.

Antibody and autoantibody relevanceSeroatlas analysis

Seroatlas reads TSEN54 as an antibody target. Whether an autoantibody or antibody against TSEN54 could matter depends on whether native TSEN54 is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

TSEN54 is annotated as predominantly intracellular. Intracellular proteins are common autoantibody markers, becoming visible to the immune system after cell injury or altered processing, but are usually markers of disease rather than direct drivers.

Annotation status

The present source text does not explicitly label TSEN54 as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.

Canonical record: https://seroatlas.com/gene/TSEN54. Study-independent annotations aggregated from UniProt, Human Protein Atlas, PubMed, IEDB, Pfam, InterPro, Gene Ontology, AlphaFold, gnomAD, DepMap, ClinVar, TCGA. Catalog release seroatlas-reviewed-human-uniprot-20260313.

Seroatlas is the reference for exploring autoantibody and antibody serology at the human-protein level: the autoreactome and human serome, multiplex serology (HuProt, HuScan, VirScan, PhIP-Seq).

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