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Genetic epilepsy syndromes

Gene: SIX3

Amber List (moderate evidence)

SIX3 (SIX homeobox 3)
EnsemblGeneIds (GRCh38): ENSG00000138083
EnsemblGeneIds (GRCh37): ENSG00000138083
OMIM: 603714, Gene2Phenotype
SIX3 is in 10 panels

4 reviews

Rebecca Foulger (Genomics England curator)

I don't know

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: Alison Callaway and John Taylor. 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

Some evidence. This gene appears to be associated with holoprosencephaly where seizures can ben a feature.
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
Holoprosencephaly 2, 157170; Schizencephaly, 269160

Publications

Sarah Leigh (Genomics England Curator)

Comment on publications: PMID 18791198 discusses incomplete penetrance.
Created: 11 Dec 2018, 10:09 a.m.
Comment when marking as ready: Associated with relevant phenotype in OMIM and as confirmed Gen2Phen gene, however, seizures have only been reported in two cases of SIX3 variant carriers. In PMID: 20157829, patient 4 had a seizure but certain epilepsy characteristic activity in the subsequent electroencephalogram (EEG) was not met. The variants (c.618C>A + c.621G>A; p.Gly206Gly + p.Glu207Glu) were found in this case. The synonymous variant c.621G>A, was not predicted to effect splicing, although it was was predicted to create a consensus sequence motif for an additional SF2/ASF (score 2.71378; threshold 1.956) as well as SRp40 (score 2.98263; threshold 2.67) splice enhancer. Both consensus sequences are recognized by the human proteins SF2/ASF or SRp40, respectively, and are important for the recognition and utilization of regular as well as alternative splice sites (Wang et al. 2005), and these may be considered to be pathogenic.
In PMID 28670735 a deletion of SIX3 gene was reported in a case with seizures, but incomplete penetrance has been suggested. The publication PMID 19346217 mentions seizures as a clinical feature, however, precise details about cases cannot be found as the supplementary material tables 1a & b are no longer available (the authors have been contacted, December 2018).
Created: 11 Dec 2018, 10 a.m.
Comment on publications: Variants reported in following articles in either Holoprosencephaly 2 157170 or Schizencephaly 269160 however, seizures are not mentioned in the patients being reported PMID: 19353631, 17001667, 10369266, 15523651.
Created: 4 Dec 2018, 5:09 p.m.
Comment on phenotypes: Schizencephaly 269160
Created: 4 Dec 2018, 12:14 p.m.

Zornitza Stark (Australian Genomics)

Green List (high evidence)

Seizures are part of the phenotype of this brain development disorder.
Created: 21 Aug 2018, 9:30 a.m.

Mode of inheritance
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted

Phenotypes
Holoprosencephaly 2, MIM#157170

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

Details

Mode of Inheritance
MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Sources
  • Wessex and West Midlands GLH
  • NHS GMS
  • Expert Review Amber
  • Literature
Phenotypes
  • Holoprosencephaly 2 157170
  • Schizencephaly 269160
OMIM
603714
Clinvar variants
Variants in SIX3
Penetrance
Incomplete
Publications
Panels with this gene

History Filter Activity

6 Aug 2019, Gel status: 2

Added New Source

Rebecca Foulger (Genomics England curator)

Source Wessex and West Midlands GLH was added to SIX3.

6 Aug 2019, Gel status: 2

Added New Source

Rebecca Foulger (Genomics England curator)

Source NHS GMS was added to SIX3.

11 Dec 2018, Gel status: 2

Panel promoted to version 1.0

Sarah Leigh (Genomics England Curator)

Zornitza Stark: Seizures are part of the pheno

11 Dec 2018, Gel status: 2

Set publications

Sarah Leigh (Genomics England Curator)

Publications for gene: SIX3 were set to 28670735; 20157829; 19346217

11 Dec 2018, Gel status: 2

Entity classified by Genomics England curator

Sarah Leigh (Genomics England Curator)

Gene: six3 has been classified as Amber List (Moderate Evidence).

11 Dec 2018, Gel status: 2

Set publications

Sarah Leigh (Genomics England Curator)

Publications for gene: SIX3 were set to 28670735; 20157829

4 Dec 2018, Gel status: 2

Set publications

Sarah Leigh (Genomics England Curator)

Publications for gene: SIX3 were set to 28670735; 20157829

4 Dec 2018, Gel status: 2

Set publications

Sarah Leigh (Genomics England Curator)

Publications for gene: SIX3 were set to

4 Dec 2018, Gel status: 2

Removed Source, Added New Source, Set penetrance

Sarah Leigh (Genomics England Curator)

Source Victorian Clinical Genetics Services was removed from SIX3. Source Literature was added to SIX3. Penetrance for gene SIX3 was set from to None

4 Dec 2018, Gel status: 2

Set Phenotypes

Sarah Leigh (Genomics England Curator)

Phenotypes for gene: SIX3 were changed from Holoprosencephaly 2 157170 to Holoprosencephaly 2 157170; Schizencephaly 269160

3 Dec 2018, Gel status: 2

Set Phenotypes

Sarah Leigh (Genomics England Curator)

Phenotypes for gene: SIX3 were changed from to Holoprosencephaly 2 157170

3 Dec 2018, Gel status: 2

Set mode of inheritance

Sarah Leigh (Genomics England Curator)

Mode of inheritance for gene: SIX3 was changed from to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown

25 Jun 2018, Gel status: 2

Added New Source

Sarah Leigh (Genomics England Curator)

Expert Review Amber was added to SIX3. Panel: Genetic Epilepsy Syndromes

25 Jun 2018, Gel status: 1

Added New Source

Sarah Leigh (Genomics England Curator)

SIX3 was added to Genetic Epilepsy Syndromes panel. Sources: Victorian Clinical Genetics Services

25 Jun 2018, Gel status: 1

Created

Sarah Leigh (Genomics England Curator)

SIX3 was created by Sarah Leigh