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Intellectual disability

Gene: SLC1A2

Green List (high evidence)
SLC1A2 (solute carrier family 1 member 2)
EnsemblGeneIds (GRCh38): ENSG00000110436
EnsemblGeneIds (GRCh37): ENSG00000110436
OMIM: 600300, Gene2Phenotype
SLC1A2 is in 4 panels

3 reviews

Rebecca Foulger (Genomics England curator)

Comment on list classification: Updated rating from Grey to Green. Added to panel and reviewed Green by Konstantinos Varvagiannis. As noted by Konstantinos Varvagiannis, 4 unrelated individuals reported (PMIDs:27476654, 28777935) all with profound/severe ID as a feature. Therefore sufficient cases to support a Green (diagnostic-grade) rating.
Created: 14 Feb 2019, 2 p.m.
PMID:27476654 (Epi4K Consortium) identified 2 individuals with de novo variants in SLC1A2, both with profound ID amongst their phenotypes (Table 3).

PMID:28777935 (Guella et al, 2017) report 2 individuals with de novo variants in SLC1A2. Both had ID (profound in Subject A, and severe in Subject C).
Created: 14 Feb 2019, 1:56 p.m.
Created: 14 Feb 2019, 1:56 p.m.

Panel version: 2.641

Louise Daugherty (Genomics England Curator)

Comment on phenotypes: amended formatting of MIM phenotype
Created: 19 Jan 2019, 6:41 p.m.
Created: 19 Jan 2019, 6:41 p.m.

Panel version: 2.597

Konstantinos Varvagiannis (Other)

Green List (high evidence)

Pathogenic variants in SLC1A2 cause Epileptic encephalopathy, early infantile, 41 (EIEE41 - MIM 617105).

At least 4 unrelated patients each with (private) de novo variants have been reported (PMIDs: 27476654, 28777935). ID is a universal feature.

This gene is included in gene panels for ID offered by diagnostic laboratories (incl. Radboudumc).

SLC1A2 is a probable DD gene in G2P associated with Epileptic encephalopathy.

As a result this gene could possibly be included in this panel as green if the phenotype is thought to be relevant.

Note: According to the Genetic epilepsy syndromes panel this gene was first added in the ID panel but appears to have been removed subsequently (phenotype thought to fit better the other panel). However several other "pure" EIEE genes (probably more than 20) have been included here, most rated green.

Sources: Literature, Radboud University Medical Center, Nijmegen
Created: 14 Dec 2018, 8:08 a.m.

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

Phenotypes
Epileptic encephalopathy, early infantile, 41 (MIM 617105)

Publications

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

Created: 14 Dec 2018, 8:08 a.m.

Panel version: 2.584

Details

Mode of Inheritance
MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Sources
  • Expert Review Green
Phenotypes
  • Epileptic encephalopathy, early infantile, 41, OMIM:617105
  • developmental and epileptic encephalopathy, 41, MONDO:0014916
OMIM
600300
Clinvar variants
Variants in SLC1A2
Penetrance
Complete
Publications
Panels with this gene

History Filter Activity

14 Jul 2022, Gel status: 3

Set Phenotypes

Sarah Leigh (Genomics England Curator)

Phenotypes for gene: SLC1A2 were changed from Epileptic encephalopathy, early infantile, 41, 617105; Intellectual disability to Epileptic encephalopathy, early infantile, 41, OMIM:617105; developmental and epileptic encephalopathy, 41, MONDO:0014916

14 Feb 2019, Gel status: 3

Entity classified by Genomics England curator

Rebecca Foulger (Genomics England curator)

Gene: slc1a2 has been classified as Green List (High Evidence).

14 Feb 2019, Gel status: 0

Set Phenotypes

Rebecca Foulger (Genomics England curator)

Phenotypes for gene: SLC1A2 were changed from Epileptic encephalopathy, early infantile, 41, 617105 to Epileptic encephalopathy, early infantile, 41, 617105; Intellectual disability

19 Jan 2019, Gel status: 0

Set Phenotypes

Louise Daugherty (Genomics England Curator)

Phenotypes for gene: SLC1A2 were changed from Epileptic encephalopathy, early infantile, 41 (MIM 617105) to Epileptic encephalopathy, early infantile, 41, 617105

12 Dec 2018, Gel status: 0

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

Konstantinos Varvagiannis (Other)

gene: SLC1A2 was added gene: SLC1A2 was added to Intellectual disability. Sources: Literature,Radboud University Medical Center, Nijmegen Mode of inheritance for gene: SLC1A2 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Publications for gene: SLC1A2 were set to 27476654; 28777935 Phenotypes for gene: SLC1A2 were set to Epileptic encephalopathy, early infantile, 41 (MIM 617105) Penetrance for gene: SLC1A2 were set to Complete Review for gene: SLC1A2 was set to AMBER gene: SLC1A2 was marked as current diagnostic