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Undiagnosed metabolic disorders

Gene: GNMT

Green List (high evidence)

GNMT (glycine N-methyltransferase)
EnsemblGeneIds (GRCh38): ENSG00000124713
EnsemblGeneIds (GRCh37): ENSG00000124713
OMIM: 606628, Gene2Phenotype
GNMT is in 3 panels

1 review

Sarah Leigh (Genomics England Curator)

Comment on list classification: Associated with relevant phenotype in OMIM, but not associated with phenotype in Gen2Phen. At least 3 variants reported in 2 unrelated cases, with supportive functional data.
Created: 15 Aug 2019, 10:08 a.m. | Last Modified: 15 Aug 2019, 10:08 a.m.
Panel Version: 1.152
Comment when marking as ready: Associated with phenotype in OMIM, not in G2P / DD. At least 3 variants reported in 2 cases, together with biochemical evidence for disruptive effect of variant p.(H176N)
Created: 19 Jan 2017, 1:12 p.m.

Details

Mode of Inheritance
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Green
  • Radboud University Medical Center, Nijmegen
  • UKGTN
  • Literature
Phenotypes
  • Glycine N-methyltransferase deficiency 606664
OMIM
606628
Clinvar variants
Variants in GNMT
Penetrance
Complete
Publications
Panels with this gene

History Filter Activity

15 Aug 2019, Gel status: 3

Entity classified by Genomics England curator

Sarah Leigh (Genomics England Curator)

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

15 Aug 2019, Gel status: 2

Set publications

Sarah Leigh (Genomics England Curator)

Publications for gene: GNMT were set to 27604308; 17660255

27 Feb 2017, Gel status: 2

panel promoted to version 1

Sarah Leigh (Genomics England Curator)

Construction of “Undiagnosed Metabolic Disorders” (UDM) panel • The 614 genes from the neurometabolic gene panel (PMID: 27604308) added • Green genes downloaded from V1 metabolic panels (Cerebral folate deficiency, Congenital disorders of glycosylation, Hyperammonaemia, Ketotic hypoglycaemia, Mitochondrial disorders, Mucopolysaccharideosis, Gaucher, Fabry, Peroxisomal disorders), sources replaced with "Expert review green", then loaded as a review onto UDM panel, resulting in 367 green genes and 333 red (therefore 86 new green genes included from the additional metabolic panels that weren't previously on the UDM panel) • Downloaded green genes from all panels. Removed genes from none V1 panels. Removed genes from the metabolic panels mentioned above. Compared the remaining genes with the red genes from UDM panel. Loaded as an "Expert review Amber" review to the overlapping genes, (the panel name where the genes came from was used as the phenotype) • Used variant information from PMID 27604308 to review the genes on this panel • Reviewed genes on UDM panel with genes from Emory "Inherited Metabolic Disorders: Sequencing Panel" and UKGTN “Inborn Errors of Metabolism 226 panel”, changing status where appropriate, added 14 UKGTN genes that had not be listed before • Review 10 red genes that had not previously been reviewed, 4/10 were reclassified as green • Review the remaining 145 red genes that had not previously been reviewed (shared between reviewers EM, RF, LD, AT, HB, ON & SL), resulting in 60 green, 11 amber, 70 red, 4 I don’t know reviews) • Reviewed genes from PMID: 24816252 as a publication to genes found in the Inborn error or metabolism Genes metabolomics GWAS paper (figure 5). 2 new genes added

19 Jan 2017, Gel status: 2

Gene classified by Genomics England curator

Sarah Leigh (Genomics England Curator)

This gene has been classified as Amber List (Moderate Evidence).

19 Jan 2017, Gel status: 2

Set publications

Sarah Leigh (Genomics England Curator)

Publications for GNMT were set to 27604308; 17660255

19 Jan 2017, Gel status: 2

Upload gene information

Sarah Leigh (Genomics England Curator)

GNMT was added to Undiagnosed metabolic disorderspanel. Sources: Radboud University Medical Center, Nijmegen,UKGTN

19 Jan 2017, Gel status: 0

Set Mode of Inheritance

Sarah Leigh (Genomics England Curator)

Model of inheritance for gene GNMT was set to BIALLELIC, autosomal or pseudoautosomal

19 Jan 2017, Gel status: 0

Set Phenotypes

Sarah Leigh (Genomics England Curator)

Phenotypes for gene GNMT were set to Glycine N-methyltransferase deficiency 606664

28 Oct 2016, Gel status: 0

Added New Source

Sarah Leigh (Genomics England Curator)

GNMT was added to Undiagnosed metabolic disorderspanel. Sources: Literature

28 Oct 2016, Gel status: 0

Created

Sarah Leigh (Genomics England Curator)

GNMT was created by sleigh