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Intellectual disability

Gene: TSEN34

Green List (high evidence)
TSEN34 (tRNA splicing endonuclease subunit 34)
EnsemblGeneIds (GRCh38): ENSG00000170892
EnsemblGeneIds (GRCh37): ENSG00000170892
OMIM: 608754, Gene2Phenotype
TSEN34 is in 11 panels

3 reviews

Ida Ertmanska (Genomics England Curator)

I don't know

Comment on list classification: There is one patient reported in literature with a biallelic variant in TSEN34 and Pontocerebellar hypoplasia type 2. While TSEN34 shares a biochemical function with other genes known to cause Pontocerebellar hypoplasia type 2, the clinical evidence for this gene-disease association is lacking in literature. Hence, TSEN34 should be demoted to Amber for Intellectual disability until more evidence emerges.
Created: 16 Dec 2025, 8:36 a.m. | Last Modified: 29 Dec 2025, 11:50 a.m.
Panel Version: 9.206
PMID: 20952379 Namavar et al., 2011
Reported one Pontocerebellar hypoplasia type 2C patient with a homozygous p.R58W variant in TSEN34 and epileptic seizures. PCH2 patient with seizures and TSEN34 variant reported in (most likely the same patient as in PMID:18711368 Budde et al., 2008). Sequenced exon-intron boundaries of TSEN54, TSEN34, TSEN2, TSEN15, RARS2 and VRK1 only.
Patient details from PMID:18711368: Patient hg1, male, phenotype: progressive microcephaly, chorea/dystonia, visual impairment, spontaneous breath; MRI typical.

PMID: 27370523 Balbi, Taicher & Litman, 2016
Brief mention of a 2-year-old female child diagnosed with TSEN34-related pontocerebellar hypoplasia Type 2 - no variant/clinical details.

Functional evidence:
PMID: 32476018 Hayne et al., 2020 / PMID: 37544645 Hayne et al., 2023
Human tRNA splicing endonuclease (TSEN) is comprised of four core subunits (TSEN54, TSEN2, TSEN34 and TSEN15), and it co-purifies with CLP1. Other TSEN subunits and CLP1 are all known to cause PCH. The TSEN34 R58W mutation eliminates a salt bridge between R58 and E218, affecting protein stability.

Additional info:
Variant NM_001077446.4(TSEN34):c.862_865dup (p.Leu289fs) was reported as Likely Pathogenic for Pontocerebellar hypoplasia type 2C in ClinVar by Mendelics (source: clinical testing).

This gene is putatively linked to AR Pontocerebellar hypoplasia type 2C, MIM:612390 (OMIM accessed 16th Dec 2025).
Created: 16 Dec 2025, 8:35 a.m. | Last Modified: 16 Dec 2025, 8:38 a.m.
Panel Version: 9.198

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Phenotypes
Pontocerebellar hypoplasia type 2C, OMIM:612390; pontocerebellar hypoplasia type 2C, MONDO:0012891

Publications

Created: 16 Dec 2025, 8:35 a.m.
Last Modified: 29 Dec 2025, 11:50 a.m.
Panel version: 9.196

Caroline Wright (Sanger)

Green List (high evidence)

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Phenotypes
PONTOCEREBELLAR HYPOPLASIA TYPE 2 AND TYPE 4

Publications

  • 0

Created: 5 Nov 2017, 2:42 a.m.

Panel version: 0

Lu Raymond (university of cambridge )

Green List (high evidence)

Created: 23 Feb 2016, 10:40 a.m.

Panel version: 0.306

Details

Mode of Inheritance
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Green
Phenotypes
  • Pontocerebellar hypoplasia type 2C, OMIM:612390
  • pontocerebellar hypoplasia type 2C, MONDO:0012891
Tags
Q4_25_demote_amber
OMIM
608754
Clinvar variants
Variants in TSEN34
Penetrance
Complete
Publications
Panels with this gene

History Filter Activity

16 Dec 2025, Gel status: 3

Set Phenotypes

Ida Ertmanska (Genomics England Curator)

Phenotypes for gene: TSEN34 were changed from PONTOCEREBELLAR HYPOPLASIA TYPE 2 AND TYPE 4 to Pontocerebellar hypoplasia type 2C, OMIM:612390; pontocerebellar hypoplasia type 2C, MONDO:0012891

16 Dec 2025, Gel status: 3

Set publications

Ida Ertmanska (Genomics England Curator)

Publications for gene: TSEN34 were set to 0

16 Dec 2025, Gel status: 3

Added Tag

Ida Ertmanska (Genomics England Curator)

Tag Q4_25_demote_amber tag was added to gene: TSEN34.

12 Mar 2018, Gel status: 3

Panel promoted to version 2.0

Ellen McDonagh (Genomics England Curator)

12.03.2018: Due to major updates completed (Phase 1, 2 and 3), this panel was promoted to Version 2 in order to reflect the major updates since November 2017 which have resulted in reviews for 836 genes added by Genomics England Curators and the Clinical Team, 130 new Green genes added to the interpretation pipeline (from 751 to 881 Green genes), and the gene total has increased from 1879 to 1927.

13 Nov 2015, Gel status: 4

gel status update

GEL ()

The Gel status was updated for this whole panel

13 Nov 2015, Gel status: 4

gel status update

GEL ()

The Gel status was updated for this whole panel

13 Nov 2015, Gel status: 0

Added New Source

Ellen McDonagh (Genomics England Curator)

TSEN34 was added to Intellectual disabilitypanel. Sources: Expert Review Green

13 Nov 2015, Gel status: 0

Created

Ellen McDonagh (Genomics England Curator)

TSEN34 was created by ellenmcdonagh