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Hereditary neuropathy NOT PMP22 copy number

Gene: ATL3

Amber List (moderate evidence)

ATL3 (atlastin GTPase 3)
EnsemblGeneIds (GRCh38): ENSG00000184743
EnsemblGeneIds (GRCh37): ENSG00000184743
OMIM: 609369, Gene2Phenotype
ATL3 is in 5 panels

7 reviews

Alexander Rossor (UCL Institute of Neurology)

Green List (high evidence)

Autosomal dominant HSN, several families described . Previous recessive entry was an error
Created: 16 May 2019, 12:02 p.m.

Mode of inheritance
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted

Natalie Forrester (SWGLH - Bristol Genetics)

I don't know

Literature search 6th May 2016, 2 articles found PMID: 24459106 c.575A>G (p.Tyr192Cys) heterozygous segregated with affected family members in a German family and Spanish family with hereditary sensory and autonomic neuropathies type 1, Haplotype analysis at the ATL3 locus of both families suggested that they share the same alleles compatible with identity by descent; PMID:24736309 - report of a Bosnian family, in which father and son with hereditary sensory neuropathy type 1 were heterozygous for ATL3 c.1013C>G p.Pro338Arg, that was not found in unaffected son
Created: 29 Apr 2019, 12:30 p.m.

Mode of inheritance
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted

Publications

Louise Daugherty (Genomics England Curator)

I don't know

Gene rated Amber : From feedback from Genomics England Clinical team (Anna de Burca and Meriel McEntagart). Re-evaluation of evidence - demotion / Limited evidence highlighted by Natalie - same variant in 2 families and other variant didn't segregate - downgrade to Amber? Agree downgrade due to lack of evidence
Created: 6 Dec 2019, 2:16 p.m. | Last Modified: 6 Dec 2019, 2:16 p.m.
Panel Version: 0.35
Comment on list classification: This gene has changed ratings because the panel for R78 was going to be a broad panel (to include conditions where neuropathy is part of a more complex phenotype or where there is overlap with another neurological presentation eg. HSP) 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, which this panel represents. For genes that represent the broader phenotype see https://panelapp.genomicsengland.co.uk/panels/85/.
Created: 6 Dec 2019, 1:17 p.m. | Last Modified: 6 Dec 2019, 1:17 p.m.
Panel Version: 0.8
Rating and review submitted on behalf of James Polke (Neurogenetics Laboratory,Institute of Neurology, London), on behalf of London North GLH for GMS Neurology specialist test group.
Created: 9 May 2019, 5 p.m.
Review and rating submitted by Natalie Forrester (SWGLH - Bristol Genetics) on behalf of South West GLH for GMS Neurology specialist test group.
Created: 29 Apr 2019, 12:53 p.m.

James Polke (Neurogenetics Laboratory, Institute of Neurology, London)

Green List (high evidence)

Mary Reilly (Institute of Neurology)

Green List (high evidence)

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Richard Scott (Genomics England Curator)

Comment when marking as ready: 24459106 and 24736309 both demonstrate monoallelic (AD) inheritance
Created: 8 Jul 2016, 3:22 a.m.

Ellen McDonagh (Genomics England Curator)

Comment on mode of inheritance: The literature reports and OMIM state monoallelic inheritance (variants found in a heterozygous state), but both reviewers suggested biallelic.
Created: 6 May 2016, 8:26 a.m.
Comment on list classification: A reviewer added the gene, and a second reviewer rated this green.
Created: 6 May 2016, 8:24 a.m.

Details

Mode of Inheritance
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Sources
  • Expert Review Amber
  • Expert Review
  • South West GLH
  • London North GLH
  • NHS GMS
  • South West GLH
  • NHS GMS
  • London North GLH
OMIM
609369
Clinvar variants
Variants in ATL3
Penetrance
None
Publications
Panels with this gene

History Filter Activity

6 Dec 2019, Gel status: 2

Entity classified by Genomics England curator

Louise Daugherty (Genomics England Curator)

Gene: atl3 has been classified as Amber List (Moderate Evidence).

5 Dec 2019, Gel status: 3

Created, Added New Source, Set mode of inheritance, Set publications

Ellen McDonagh (Genomics England Curator)

gene: ATL3 was added gene: ATL3 was added to Hereditary neuropathy NOT PMP22 copy number. Sources: NHS GMS,London North GLH,South West GLH,Expert Review Green,Expert Review Mode of inheritance for gene: ATL3 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Publications for gene: ATL3 were set to 24459106; 24736309