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Genetic epilepsy syndromes

Gene: SLC1A4

Green List (high evidence)

SLC1A4 (solute carrier family 1 member 4)
EnsemblGeneIds (GRCh38): ENSG00000115902
EnsemblGeneIds (GRCh37): ENSG00000115902
OMIM: 600229, Gene2Phenotype
SLC1A4 is in 6 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: John Taylor and Helen Lord. Suggested gene rating: Green.
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)

Green List (high evidence)

AR spastic tetraplegia, thin corpus callosum and progressive microcephaly - some patients may have seizures. Srour et al, 2015 - 2 sibs - consanguineous AJ parents - 1 had seizures. Heimer et al, 2015, 2 unrelated children. 1 of AJ descent and the other of Ashkenazi-Iraqi parents - both had epilepsy. Damseh et al, 2015 - 10 children from 8 families of AJ descent - 5 of which developed seizures. Common AJ variant E256K. In vitro studies show that the E256K variant reduces L-serine and L-alanine transport by 25% and 20% respectively. Another variant R457W - same functional work showed no measurable substrate transport activity. Pironti et al, 2018 - novel hom variant identifed in an Italian boy - had epilepsy. Conroy et al, 2016 - hom nonsense variant detected in an Irish proband who had seizures.
Created: 6 Aug 2019, 8:31 p.m. | Last Modified: 6 Aug 2019, 8:31 p.m.
Panel Version: 1.188

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Phenotypes
Spastic tetraplegia, thin corpus callosum, and progressive microcephaly, 616657

Publications

Sarah Leigh (Genomics England Curator)

Comment when marking as ready: Associated with phenotype in OMIM and not in Gen2Phen. Single variant originally only recorded in cases with Ashkenazi Jewish heritage, this variant and at least two others have now been reported in additional unrelated cases from other populations.
Created: 26 Sep 2018, 10:13 a.m.

Zornitza Stark (Australian Genomics)

Green List (high evidence)

Multiple affected individuals reported in the literature, seizures/EE are part of the phenotype. While initial reports identified a recurrent missense variant in individuals of Ashkenazi Jewish ancestry, there have been more recent reports of individuals from other ethnic backgrounds with different variants. Gene is also relevant to the ID panel.
Created: 4 Sep 2018, 3:29 a.m.

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Phenotypes
Spastic tetraplegia, thin corpus callosum, and progressive microcephaly, MIM# 616657

Publications

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

Details

Mode of Inheritance
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Wessex and West Midlands GLH
  • NHS GMS
  • Expert Review Green
Phenotypes
  • Spastic tetraplegia, thin corpus callosum, and progressive microcephaly, 616657
OMIM
600229
Clinvar variants
Variants in SLC1A4
Penetrance
None
Publications
Panels with this gene

History Filter Activity

6 Aug 2019, Gel status: 3

Added New Source

Rebecca Foulger (Genomics England curator)

Source Wessex and West Midlands GLH was added to SLC1A4.

6 Aug 2019, Gel status: 3

Added New Source

Rebecca Foulger (Genomics England curator)

Source NHS GMS was added to SLC1A4.

11 Dec 2018, Gel status: 3

Panel promoted to version 1.0

Sarah Leigh (Genomics England Curator)

Zornitza Stark: Multiple affected individuals

26 Sep 2018, Gel status: 3

Entity classified by Genomics England curator

Sarah Leigh (Genomics England Curator)

Gene: slc1a4 has been classified as Green List (High Evidence).

26 Sep 2018, Gel status: 3

Entity classified by Genomics England curator

Sarah Leigh (Genomics England Curator)

Gene: slc1a4 has been classified as Green List (High Evidence).

26 Sep 2018, Gel status: 0

Set Phenotypes

Sarah Leigh (Genomics England Curator)

Phenotypes for gene: SLC1A4 were changed from Spastic tetraplegia, thin corpus callosum, and progressive microcephaly, MIM# 616657 to Spastic tetraplegia, thin corpus callosum, and progressive microcephaly, 616657

4 Sep 2018, Gel status: 0

Added New Source

Zornitza Stark (Australian Genomics)

SLC1A4 was added to Genetic Epilepsy Syndromes panel. Sources: Expert Review

4 Sep 2018, Gel status: 0

Created

Zornitza Stark (Australian Genomics)

SLC1A4 was created by Zornitza Stark