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Genetic epilepsy syndromes

Gene: SETD5

Amber List (moderate evidence)

SETD5 (SET domain containing 5)
EnsemblGeneIds (GRCh38): ENSG00000168137
EnsemblGeneIds (GRCh37): ENSG00000168137
OMIM: 615743, Gene2Phenotype
SETD5 is in 5 panels

7 reviews

Rebecca Foulger (Genomics England curator)

I don't know

As discussed with members of the GMS Neurology Specialist Test Group on the Webex call Thursday 8th August 2019 for Clinical Indication R59 Early onset or syndromic epilepsy: Agreed that there is insufficient evidence to rate this gene Green, and an Amber rating is appropriate. Demoted from Green to Amber.
Created: 15 Aug 2019, 9:38 a.m. | Last Modified: 15 Aug 2019, 9:38 a.m.
Panel Version: 1.226
Re-reviewed this gene when curating panel for GMS Clinical Indication R59 Early onset or syndromic epilepsy. In summary: although four reviewers agreed it should be on EE panel, there is limited evidence of a seizure phenotype. PMID:26482601: (Kobayashi et al., 2016) examined 11 patients with early-onset epileptic encephalopathy, and SETD5 variants were amongst the findings. Therefore consider demoting SETD5.
Created: 15 Aug 2019, 9:37 a.m. | Last Modified: 15 Aug 2019, 10:29 a.m.
Panel Version: 1.236
Review and rating collated by Tracy Lester (Oxford Medical Genetics Laboratories Oxford University Hospitals NHS Foundation Trust, 2019_02_06) on behalf of Wessex and West Midlands GLH for GMS Neurology specialist test group, for Clinical Indication R59 'Early onset or syndromic epilepsy'. Review contributors: John Taylor and Helen Lord. Suggested gene rating: Amber.
Created: 6 Aug 2019, 8:38 p.m. | Last Modified: 6 Aug 2019, 8:38 p.m.
Panel Version: 1.189

Tracy Lester (Genetics laboratory, Oxford UK)

I don't know

AD mental retardation - no mention of seizures as a clinical feature on OMIM. Panel app - have as a green gene seems to be due to it being in an EIEE panel?? On HGMD pro one mention of a mutation assoc with dev delay, seizures, delayed speech and dysmorphic features - Halvardson et al 2016 - opened paper and the SETD5 variant was in a patient with AD MR. Don't add to panel.
Created: 6 Aug 2019, 8:31 p.m. | Last Modified: 6 Aug 2019, 8:31 p.m.
Panel Version: 1.188

Mode of inheritance
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted

Phenotypes
Mental retardation, 615761

Publications

Amy McTague (UCL Institute of Child Health)

Green List (high evidence)

Mode of inheritance
MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown

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

Natalie Trump (NHS - Great Ormond Street Hospital)

Green List (high evidence)

Mode of inheritance
MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown

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

Manju Kurian (UCL-Institute of Child Health)

Green List (high evidence)

Mode of inheritance
MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown

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

Richard Scott (North Thames GMC/UCL)

Green List (high evidence)

Mode of inheritance
MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown

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

Ellen McDonagh (Genomics England Curator)

Comment when marking as ready: Confirmed DD gene and all 4 reviewers agree this should be green. Mode of inheritance and loss-of-function mechanism confirmed.
Created: 21 Jan 2016, 12:59 p.m.
Comment on phenotypes: Source: OMIM
Created: 21 Jan 2016, 12:57 p.m.
Comment on mode of inheritance: Confirmed and not on imprinted gene list.
Created: 21 Jan 2016, 12:57 p.m.

Details

Mode of Inheritance
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Sources
  • Expert Review Amber
  • Wessex and West Midlands GLH
  • NHS GMS
  • Victorian Clinical Genetics Services
  • Expert Review
Phenotypes
  • Mental retardation, autosomal dominant 23, 615761
OMIM
615743
Clinvar variants
Variants in SETD5
Penetrance
None
Publications
Panels with this gene

History Filter Activity

28 Oct 2019, Gel status: 2

Set Phenotypes

Rebecca Foulger (Genomics England curator)

Phenotypes for gene: SETD5 were changed from Mental retardation, autosomal dominant 23 to Mental retardation, autosomal dominant 23, 615761

28 Oct 2019, Gel status: 2

Set publications

Rebecca Foulger (Genomics England curator)

Publications for gene: SETD5 were set to

15 Aug 2019, Gel status: 2

Entity classified by Genomics England curator

Rebecca Foulger (Genomics England curator)

Gene: setd5 has been classified as Amber List (Moderate Evidence).

15 Aug 2019, Gel status: 2

Entity classified by Genomics England curator

Rebecca Foulger (Genomics England curator)

Gene: setd5 has been classified as Amber List (Moderate Evidence).

6 Aug 2019, Gel status: 3

Added New Source

Rebecca Foulger (Genomics England curator)

Source Wessex and West Midlands GLH was added to SETD5.

6 Aug 2019, Gel status: 3

Added New Source

Rebecca Foulger (Genomics England curator)

Source NHS GMS was added to SETD5.

11 Dec 2018, Gel status: 4

Panel promoted to version 1.0

Sarah Leigh (Genomics England Curator)

Ellen McDonagh: Comment on mode of inheritance

25 Jun 2018, Gel status: 4

Added New Source

Sarah Leigh (Genomics England Curator)

Victorian Clinical Genetics Services was added to SETD5. Panel: Genetic Epilepsy Syndromes

4 Apr 2018, Gel status: 4

Added New Source

Sarah Leigh (Genomics England Curator)

SETD5 was added to Genetic Epilepsy Syndromes panel. Sources: Expert Review Green,Expert Review

4 Apr 2018, Gel status: 4

Created

Sarah Leigh (Genomics England Curator)

SETD5 was created by Sarah Leigh