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Intellectual disability

Gene: TRMT1

Green List (high evidence)

TRMT1 (tRNA methyltransferase 1)
EnsemblGeneIds (GRCh38): ENSG00000104907
EnsemblGeneIds (GRCh37): ENSG00000104907
OMIM: 611669, Gene2Phenotype
TRMT1 is in 4 panels

5 reviews

Louise Daugherty (Genomics England Curator)

As a result of watchlist tag audit the watchlist tag was removed from TRMT1- this is now a green gene with sufficient evidence/review. Noted as being removed but this was not updated in the database.
Created: 13 Jan 2020, 4:19 p.m. | Last Modified: 13 Jan 2020, 4:19 p.m.
Panel Version: 3.0

Konstantinos Varvagiannis (Other)

Green List (high evidence)

PMID: 30289604 reports on 4 additional patients from 2 unrelated consanguineous Pakistani families.

One subject was homozygous for a previously described frameshift variant. Affected individuals from the second family were homozygous for a novel splice-site variant.

The phenotype of the new patients as well as of previously published ones (PMID: 21937992, 26308914) is summarized.

In total 9 individuals from 4 families have been reported. ID was a universal feature (9/9). Seizures have been reported in 4 individuals from 2 families. Primary microcephaly was observed in the 4 new patients but was not the case for the rest of the cohort.

3 loss-of-function variants have been observed in total.

PMID: 28784718 provides extensive functional evidence for the 2 variants reported in 3 of the families.

TRMT1 is included in gene panels for intellectual disability offered by different diagnostic laboratories.

As a result, this gene can be considered for upgrade to green.
Created: 5 Dec 2018, 2:34 p.m.

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Phenotypes
Global developmental delay; Intellectual disability; Seizures; Microcephaly

Publications

Variants in this GENE are reported as part of current diagnostic practice

Caroline Wright (Sanger)

Red List (low evidence)

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Phenotypes
AUTOSOMAL RECESSIVE MENTAL RETARDATION

Publications

Rebecca Foulger (Genomics England curator)

I don't know

Removed 'watchlist' tag following promotion of gene rating from Amber to Green.
Created: 14 May 2019, 1:35 p.m.
Comment on list classification: Updated rating from Amber to Green based on the additional recent publication provided by Konstantinos Varvagiannis. PMID:30289604 (Blaesius et al., 2018) report 4 further patients from 2 unrelated consanguineous Pakistani families with homozygous variants in TRMT1 (a 32 bp deletion, and a G>T transversion predicted to result in aberrant splicing and LOF). All four patients had mild-to -moderate intellectual disability. This brings the total number of unrelated cases to four (the previous two cases coming from PMIDs:21937992 and PMID:26308914) . With functional studies in PMID:28784718 (Dewe et al., 2017), there is now sufficient evidence for a Green (diagnostic-grade) rating.
Created: 14 May 2019, 1:30 p.m.
2 Iranian families reported so far with TRMT1 variants and autosomal recessive ID from PMID:21937992 (2011) and PMID:26308914 (2015). Possible DD-G2P gene for AUTOSOMAL RECESSIVE MENTAL RETARDATION. Rated as Amber because further cases required to rate as diagnostic-grade.
Created: 29 Nov 2017, 11:19 a.m.
Added 'watchlist' tag to collect further publications (in addition to PMID:21937992 and PMID:26308914) to support ID causation.
Created: 5 Oct 2017, 2:43 p.m.

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Phenotypes
autosomal recessive intellectual disorder; ARID

Publications

Lu Raymond (university of cambridge )

Red List (low evidence)

Details

Mode of Inheritance
BIALLELIC, autosomal or pseudoautosomal
Sources
Phenotypes
  • autosomal recessive intellectual disorder
  • ARID
  • Mental retardation, autosomal recessive 68, 618302
  • Global developmental delay
  • Intellectual disability
OMIM
611669
Clinvar variants
Variants in TRMT1
Penetrance
Complete
Publications
Panels with this gene

History Filter Activity

13 Jan 2020, Gel status: 3

Removed Tag

Louise Daugherty (Genomics England Curator)

Tag watchlist was removed from gene: TRMT1.

14 May 2019, Gel status: 3

Set Phenotypes

Rebecca Foulger (Genomics England curator)

Phenotypes for gene: TRMT1 were changed from autosomal recessive intellectual disorder; ARID to autosomal recessive intellectual disorder; ARID; Mental retardation, autosomal recessive 68, 618302; Global developmental delay; Intellectual disability

14 May 2019, Gel status: 3

Set publications

Rebecca Foulger (Genomics England curator)

Publications for gene: TRMT1 were set to 21937992; 26308914

14 May 2019, Gel status: 3

Entity classified by Genomics England curator

Rebecca Foulger (Genomics England curator)

Gene: trmt1 has been classified as Green List (High Evidence).

12 Mar 2018, Gel status: 2

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.

29 Nov 2017, Gel status: 2

Added New Source, Set publications

Ellen McDonagh (Genomics England Curator)

Expert Review Amber was added to TRMT1. Panel: Intellectual disability Publications for gene TRMT1 was set to ['21937992', ' 26308914']

13 Nov 2015, Gel status: 1

gel status update

GEL ()

The Gel status was updated for this whole panel

13 Nov 2015, Gel status: 2

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)

TRMT1 was added to Intellectual disabilitypanel. Sources: Expert Review Red

13 Nov 2015, Gel status: 0

Created

Ellen McDonagh (Genomics England Curator)

TRMT1 was created by ellenmcdonagh