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Intellectual disability

Gene: GABRA2

Green List (high evidence)

GABRA2 (gamma-aminobutyric acid type A receptor alpha2 subunit)
EnsemblGeneIds (GRCh38): ENSG00000151834
EnsemblGeneIds (GRCh37): ENSG00000151834
OMIM: 137140, Gene2Phenotype
GABRA2 is in 3 panels

2 reviews

Rebecca Foulger (Genomics England curator)

Comment on list classification: Updated rating from Grey to Green: GABRA2 was added to the panel and rated Green by Konstantinos Varvagiannis. Not yet associated with a disorder in Gene2Phenotype but there are sufficient cases from from the literature (PMIDs:29422393, 29961870, 31032849, https://doi.org/10.1101/678219) of GABRA2 variants associated with developmental delay/intellectual disability.
Created: 20 Sep 2019, 12:46 p.m. | Last Modified: 20 Sep 2019, 12:46 p.m.
Panel Version: 2.1025
Summary of evidence (refer to Konstantinos Varvagiannis' review for further details):

PMID:29422393, Orenstein et al., 2018 report a male of unrelated Ashkenazi Jewish parents with EIEE-78 and a de novo heterozygous variant in GABRA2 (N335H). Development was severely delayed. Functional studies were not performed but the variant was absent in ExAC and gnomAD controls.

PMID:29961870, Butler et al. 2018 report an 11 year old girl with EIEE-78 and a de novo heterozygous variant in GABRA2 (T292K). Development was delayed, the patient was nonverbal and had profound intellectual disability plus microcephaly.

PMID:31032849, Maljevic et al., 2019 decribe 5 patients (3 sporadic cases and 2 siblings) with four novel de novo GABRA2 missense variants (Val284Ala, Leu291Val, Met263Thr, Phe325Leu). All patients showed some degree of ID (mild to profound).

https://doi.org/10.1101/678219: Sanchis-Juan et al., 2019 identified a de novo missense variant in GABRA2 gene (Pro280Leu) in a 10 year old girl with EIEE and developmental delay. At age-10, she had severe
impairment of language, hand stereotypies, disruptive behavior and repetitive movements.
Created: 20 Sep 2019, 12:46 p.m. | Last Modified: 20 Sep 2019, 12:46 p.m.
Panel Version: 2.1024
Added 'missense' tag: all variants reported so far are missense.
Created: 20 Sep 2019, 12:44 p.m. | Last Modified: 20 Sep 2019, 12:44 p.m.
Panel Version: 2.1024

Konstantinos Varvagiannis (Other)

Green List (high evidence)

Heterozygous pathogenic GABRA2 variants cause Epileptic encephalopathy, early infantile, 78 (MIM 618557) [new OMIM entry].

At least 8 relevant individuals have been reported to date in the following studies:
- Orenstein et al. (2018 - PMID: 29422393) - 1 individual
- Butler et al. (2018 - PMID: 29961870) - 1 subject
- Maljevic et al. (2019 - PMID: 31032849 - 3 unrelated children as well as 2 affected sibs
- Sanchis-Juan et al. (2019 - bioRxiv / https://doi.org/10.1101/678219) - 1 further patient

In all affected individuals the variants were missense and - in almost all cases - had occurred as de novo events. The 2 sibs reported by Maljevic however, had inherited a missense variant from their unaffected mosaic parent.

Clinical descriptions for individuals from the 3 studies are provided in OMIM and also summarized, Maljevic - Table 1 (7 patients) and/or in the suppl. table 1 by Sanchis-Juan et al. (8 patients) (https://www.biorxiv.org/content/biorxiv/early/2019/06/21/678219/DC2/embed/media-2.xlsx). Seizures, DD and ID (relevant to the current panel) are among the reported features. Functional studies have been performed for most of the variants and are summarized for each one in the OMIM entry for GABRG2 and the aforementioned table as well.

The following variants have been reported (NM_000807.2): c.1003A>C - p.Asn335His (dn) / c.875C>A - Thr292Lys (dn) / c.871C>G - p.Leu291Val (dn) / c.788T>C - p.Met263Thr (dn) / c.851T>C - p.Val284Ala (dn) / c.975C>A - p.Phe325Leu (inherited from mosaic parent) / c.839C>T - p.Pro280Leu (dn - Sanchis-Juan et al).

As commented by Jenkins and Escayg (2019 - PMID: 31032848 / both among the authors of the 1st report) as well as by Sanchis-Juan et al., both loss- and gain- of function effects explain the pathogenicity of the various mutations reported to date. [In gnomAD GABRA2 has a Z-score for missense variants of 3.13 as well as a pLI of 1].
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GABRA2 is not associated with any phenotype in G2P.
This gene is not commonly included in gene panels for ID offered by diagnostic laboratories.
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As a result, GABRA2 can be considered for inclusion in the epilepsy and ID panels probably as green (several relevant individuals, several reported variants with supporting functional studies for most, etc.).

[Consider inclusion in other possibly relevant gene panels eg. for ASD which was feature in some patients at relevant age and/or among those evaluated].
Created: 8 Sep 2019, 4:17 p.m. | Last Modified: 10 Sep 2019, 7:17 a.m.
Panel Version: 2.1022

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

Phenotypes
Epileptic encephalopathy, early infantile, 78 (MIM 618557)

Publications

Details

Mode of Inheritance
MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Sources
Phenotypes
  • Epileptic encephalopathy, early infantile, 78, 618557
  • intellectual disability
  • developmental delay
Tags
missense
OMIM
137140
Clinvar variants
Variants in GABRA2
Penetrance
unknown
Publications
Panels with this gene

History Filter Activity

20 Sep 2019, Gel status: 3

Entity classified by Genomics England curator

Rebecca Foulger (Genomics England curator)

Gene: gabra2 has been classified as Green List (High Evidence).

20 Sep 2019, Gel status: 0

Set Phenotypes

Rebecca Foulger (Genomics England curator)

Phenotypes for gene: GABRA2 were changed from Epileptic encephalopathy, early infantile, 78, 618557) to Epileptic encephalopathy, early infantile, 78, 618557; intellectual disability; developmental delay

20 Sep 2019, Gel status: 0

Added Tag

Rebecca Foulger (Genomics England curator)

Tag missense tag was added to gene: GABRA2.

20 Sep 2019, Gel status: 0

Set Phenotypes

Rebecca Foulger (Genomics England curator)

Phenotypes for gene: GABRA2 were changed from Epileptic encephalopathy, early infantile, 78 (MIM 618557) to Epileptic encephalopathy, early infantile, 78, 618557)

8 Sep 2019, Gel status: 0

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

Konstantinos Varvagiannis (Other)

gene: GABRA2 was added gene: GABRA2 was added to Intellectual disability. Sources: Literature Mode of inheritance for gene: GABRA2 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Publications for gene: GABRA2 were set to 29422393; 29961870; 31032849; 31032848; doi.org/10.1101/678219 Phenotypes for gene: GABRA2 were set to Epileptic encephalopathy, early infantile, 78 (MIM 618557) Penetrance for gene: GABRA2 were set to unknown Review for gene: GABRA2 was set to GREEN