Genes in panel

Hereditary neuropathy

Gene: AGXT

Amber List (moderate evidence)

AGXT (alanine-glyoxylate aminotransferase)
EnsemblGeneIds (GRCh38): ENSG00000172482
EnsemblGeneIds (GRCh37): ENSG00000172482
OMIM: 604285, Gene2Phenotype
AGXT is in 11 panels

2 reviews

Louise Daugherty (Genomics England Curator)

I don't know

The Neurology Specialist Test Group agreed that this gene was recommended for the WGS panel based on a broader phenotype view to include conditions where neuropathy is part of a more complex phenotype or where there is overlap with another neurological presentation eg. HSP. This panel includes conditions where neuropathy is part of a more complex phenotype or where there is overlap with another neurological presentation. This panel as going to be used for R78, but subsequently during the follow up call on 21st June with the Test Group it was agreed that it was more clinically relevant for R78 to be restricted to genes that are associated with isolated neuropathy and as a result a new panel was created https://panelapp.genomicsengland.co.uk/panels/846/ for this purpose.
Created: 7 Dec 2019, 6:08 p.m. | Last Modified: 7 Dec 2019, 6:08 p.m.
Panel Version: 1.352
Gene remains rated as Red : From feedback from Genomics England Clinical team (Anna de Burca and Meriel McEntagart). Extension of panel scope - minor feature / Gene well established to cause PH1 Primary Hyperoxaluria (green). 2 reports of neuropathy - enough cases?- rated Red
R78 was going to be broadened to include conditions where neuropathy is part of a more complex phenotype or where there is overlap with another neurological presentation eg. HSP. Subsequently during the follow up call on 21st June with the Test Group it was agreed that it was more clinically relevant for this panel to be restricted to genes that are associated with isolated neuropathy.
Created: 5 Dec 2019, 10:52 a.m. | Last Modified: 5 Dec 2019, 11:19 a.m.
Panel Version: 1.339
Review and rating uploaded from file (Curation_Template_GMS_Neuro_AR_20190521.xlsx) submitted by Alex Rossor (UCL Institute of Neurology) on behalf of London North GLH for GMS Neurology specialist test group.
Created: 11 Jun 2019, 1:40 p.m.

Alexander Rossor (UCL Institute of Neurology)

Green List (high evidence)

Gene well established to cause PH1 (green). 2 reports of neuropathy
Created: 6 Jun 2019, 10:52 a.m.

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Phenotypes
Renal failure and deposition of calcium oxalate crystals in tissues including nerve and muscle. Sensory and motor axonal neuropathy (some slowing)

Publications

Details

Mode of Inheritance
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Amber
  • NHS GMS
  • London North GLH
Phenotypes
  • Hyperoxaluria, primary, type 1, 259900
  • Renal failure and deposition of calcium oxalate crystals in tissues including nerve and muscle. Sensory and motor axonal neuropathy (some slowing)
OMIM
604285
Clinvar variants
Variants in AGXT
Penetrance
None
Publications
Panels with this gene

History Filter Activity

7 Dec 2019, Gel status: 2

Added New Source, Status Update

Louise Daugherty (Genomics England Curator)

Source Expert Review Amber was added to AGXT. Rating Changed from Red List (low evidence) to Amber List (moderate evidence)

5 Dec 2019, Gel status: 1

Entity classified by Genomics England curator

Louise Daugherty (Genomics England Curator)

Gene: agxt has been classified as Red List (Low Evidence).

5 Dec 2019, Gel status: 3

Entity classified by Genomics England curator

Louise Daugherty (Genomics England Curator)

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

6 Jun 2019, Gel status: 1

Set publications

Louise Daugherty (Genomics England Curator)

Publications for gene: AGXT were set to

6 Jun 2019, Gel status: 1

Set Phenotypes

Louise Daugherty (Genomics England Curator)

Phenotypes for gene: AGXT were changed from to Hyperoxaluria, primary, type 1, 259900; Renal failure and deposition of calcium oxalate crystals in tissues including nerve and muscle. Sensory and motor axonal neuropathy (some slowing)

6 Jun 2019, Gel status: 1

Set mode of inheritance

Louise Daugherty (Genomics England Curator)

Mode of inheritance for gene: AGXT was changed from to BIALLELIC, autosomal or pseudoautosomal

6 Jun 2019, Gel status: 1

Added New Source

Louise Daugherty (Genomics England Curator)

Source NHS GMS was added to AGXT.

6 Jun 2019, Gel status: 1

Created, Added New Source, Set mode of inheritance

Louise Daugherty (Genomics England Curator)

gene: AGXT was added gene: AGXT was added to Hereditary neuropathy. Sources: London North GLH Mode of inheritance for gene: AGXT was set to