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Gene

TSEN2

tRNA splicing endonuclease subunit 2

Summary

Cytogenetic location
3p25.2
Coordinates
Chromosome 3: 12,484,480–12,533,658 (GRCh38)
Exons
12 exons across 49.2 kb
Protein
465 amino acids
Also known as
SEN2, SEN2L, MGC2776
MANE Select transcript
ENST00000284995.11NM_025265.4
Locus type
Protein-coding
  • Very high
  • Confident
  • Low
  • Very low

Curated report relevant to this gene

  • Spinal Muscular Atrophy

    • A group of disorders characterised by degeneration of spinal cord anterior horn cells, leading to progressive muscle weakness and atrophy.

      • 3 GenCC submitters rate it definitive or strong
      Actionability

      Gene therapy (onasemnogene abeparvovec), antisense oligonucleotide therapy (nusinersen), oral splicing modifier (risdiplam), supportive care

How TSEN2 is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
  • Stretches short reads find hard
Chromosome 3, with a bracket where TSEN2 sits. TSEN2 and 11 genes near it on chromosome 3, from 12,009,069 to 13,009,068.Chromosome 33p25.2p26.3p26.2p26.1p25.3p25.2p25.1p24.3p24.2p24.1p23p22.3p22.2p22.1p21.33p21.32p21.31p21.2p21.1p14.3p14.2p14.1p13p12.3p12.2p12.1p11.2p11.1q11.1q11.2q12.1q12.2q12.3q13.11q13.12q13.13q13.2q13.31q13.32q13.33q21.1q21.2q21.3q22.1q22.2q22.3q23q24q25.1q25.2q25.31q25.32q25.33q26.1q26.2q26.31q26.32q26.33q27.1q27.2q27.3q28q2912.2 Mb12.4 Mb12.6 Mb12.8 Mb13 MbSYN2: 12,004,325–12,192,032, forward strandSYN2TIMP4: 12,149,834–12,159,395, reverse strandTIMP4PPARG: 12,287,368–12,455,622, forward strandPPARGTSEN2: 12,484,480–12,533,658, forward strandTSEN2MKRN2OS: 12,514,934–12,561,059, reverse strandMKRN2OSMKRN2: 12,557,011–12,603,555, forward strandMKRN2RAF1: 12,582,101–12,664,201, reverse strandRAF1TMEM40: 12,733,528–12,769,457, reverse strandTMEM40CAND2: 12,796,472–12,836,433, forward strandCAND2: 12,825,768–12,871,919, forward strandRPL32: 12,834,467–12,841,587, reverse strandRPL32IQSEC1: 12,897,043–13,283,281, reverse strandIQSEC1Diagram of TSEN2: 12 exons on the forward strand of chromosome 3Exon 2: 2 known disease-causing sitesExon 3: 1 known disease-causing siteExon 5: 5 known disease-causing sitesExon 7: 4 known disease-causing sitesExon 8: 2 known disease-causing sitesExon 11: 2 known disease-causing sitesExon 12: 1 known disease-causing siteExon 1: 12,484,480–12,484,880, 401 basesExon 2: 12,489,784–12,489,989, 206 basesExon 3: 12,492,136–12,492,217, 82 basesExon 4: 12,496,518–12,496,554, 37 basesExon 5: 12,503,262–12,503,784, 523 basesExon 6: 12,505,154–12,505,231, 78 basesExon 7: 12,516,611–12,516,661, 51 basesExon 8: 12,519,059–12,519,197, 139 basesExon 9: 12,528,888–12,528,924, 37 basesExon 10: 12,529,762–12,529,873, 112 basesExon 11: 12,531,570–12,531,659, 90 basesExon 12: 12,532,662–12,533,658, 997 bases1246810125′3′

Exons of the gene's MANE Select transcript (release v1.5), from NCBI and EMBL-EBI, on the GRCh38 reference genome.

Chromosome bands from UCSC's GRCh38 ideogram (2022-10-29).

Nearby genes from Ensembl release 116, on GRCh38.

Exons make up 2.8 kb of the gene's 49.2 kb; 1,398 of those bases code for the protein.

Sequencing TSEN2

18

positions in TSEN2 where ClinVar classes a change as pathogenic or likely pathogenic

None of them falls in a region short reads find hard.

A whole genome covers all 49.2 kb of TSEN2, introns included, not only the 2.8 kb of exons.

Genes linked to the same conditions

Traits linked to TSEN2

The Human Phenotype Ontology lists these as features of the rare conditions TSEN2 can cause. Each trait's page lists the other genes linked to it.

External links

Where this comes from

  • HGNC: the gene's symbol, name, other symbols and location.
  • MANE Select v1.5, from NCBI and EMBL-EBI: the transcript, its exons and coding sequence.
  • GenCC and ClinGen, released 2026-10-17: which conditions the gene is linked to, and how strongly.
  • The ACMG secondary findings list, SF v3.2.
  • ClinVar and the GIAB stratifications: known disease-causing sites, and the regions short reads find hard.
  • The Human Phenotype Ontology, release 2026-09-01: the traits linked to the gene. Find out more at hpo.jax.org.
  • Data release 2026.10.17-8666dff2.

Cite this page

APA

Dante Labs. (n.d.). TSEN2 gene: tRNA splicing endonuclease subunit 2. Retrieved 17 October 2026, from https://dantelabs.com/genes/tsen2

Vancouver

Dante Labs. TSEN2 gene: tRNA splicing endonuclease subunit 2 [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/tsen2

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