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Intellectual disability

Gene: GABRA5

Green List (high evidence)

GABRA5 (gamma-aminobutyric acid type A receptor alpha5 subunit)
EnsemblGeneIds (GRCh38): ENSG00000186297
EnsemblGeneIds (GRCh37): ENSG00000186297
OMIM: 137142, Gene2Phenotype
GABRA5 is in 2 panels

2 reviews

Rebecca Foulger (Genomics England curator)

Comment on list classification: Upgraded from Amber to Green following advice from Genomics England clinical team. The case reported in PMID:29961870 (Butler et al 2018) had delayed milestones and is reported to be non-verbal, which is a relevant phenotype for this panel. Overall 3 unrelated cases from 2 papers.
Created: 30 Sep 2019, 1:14 p.m. | Last Modified: 30 Sep 2019, 1:14 p.m.
Panel Version: 2.1052
Comment on list classification: Updated rating from Red to Amber following external review by Konstantinos Varvagiannis. Not yet associated with a disorder in Gene2Phenotype but linked to EIEE-70 in OMIM. There are three cases from 2 publications (PMIDs 29961870 and 31056671) of GABRA5 variants associated with early infantile epileptic encephalopathy and ID. However in Butler et al., development slowed at the time of seizure onset. Therefore rating Amber awaiting further clinical input.
Created: 20 Sep 2019, 1:06 p.m. | Last Modified: 20 Sep 2019, 1:06 p.m.
Panel Version: 2.1029
Summary of recent evidence (refer to Konstantinos Varvagiannis' review for further details):

PMID:29961870, Butler et al. 2018 report a 2 year old boy (patient 1) with EIEE and a p.V294L variant in GABRA5. Cognitive and motor development slowed at the time of seizure onset. The patient developed secondary microcephaly. A de novo variant in MIA2 was also detected but was considered unlikely to contribute to the patients phenotypes due to allele frequency in the gnomAD database.

PMID:31056671, Hernandez et al. 2019 screened a cohort of patients with epilepsy and ID and report 2 individuals with GABRA5 missense variants (V294F and S413F). Both had severe ID and delayed motor development.
Created: 20 Sep 2019, 1:02 p.m. | Last Modified: 20 Sep 2019, 1:02 p.m.
Panel Version: 2.1025

Konstantinos Varvagiannis (Other)

Green List (high evidence)

Heterozygous pathogenic GABRA5 variants cause Epileptic encephalopathy, early infantile, 79 (MIM 618559) [entry recently updated in OMIM].

At least 3 relevant individuals with this diagnosis have been reported to date:

- Butler et al. (2018 - PMID: 29961870) described a 2 y.o. boy with early infantile epileptic encephalopathy (seizure onset at the age of 4m). The boy was found to harbor a de novo missense variant (NM_000810.3:c.880G>C - p.Val294Leu) identified following trio-WGS and confirmed by Sanger sequencing. Studies in HEK293 cells demonstrated expression at the surface and incorporation of the mutant subunit in the channel. The α5(V294L)β2γ2s receptors were 10 times more sensitive to GABA compared to wt, but were more likely to desensitize leading to reduced maximum GABA-evoked currents.

- Hernandez et al. (2019 - PMID: 31056671) reported on 2 unrelated individuals with early-onset epileptic encephalopathy due to de novo GABRA5 variants identified by targeted NGS sequencing (480 epilepsy-related genes):

A 3y 10m male with seizure onset at the age of 4m, severe motor delay and ID, frontotemporal atrophy and thin CC upon MRI imaging was found to harbor a de novo missense variant (NM_000810.3:c.880G>T / p.Val294Phe).

A further unrelated subject (a 7 y.o. male) with seizure onset at the age of 3 months, severe DD and ID and cortical atrophy / thin CC upon MRI imaging was heterozygous for another missense variant which had occurred as a de novo event (NM_000810.3:c.1238C>T - p.Ser413Phe).

Functional studies: Expression of HA-tagged α5(V294F) subunits at dendritic GABAergic synapses of rat hippocampal neurons was decreased compared to wt, in contrast with the expression of α5(S413F) subunits which was similar to wt. As the α5(V294F) appeared accumulated in the soma of the neurons, the authors performed additional studies – using HEK293T cells – to show that while the α5(S413F) spread outside the ER, α5(V294F) subunits localized to the ER. This was suggestive of a trafficking defect/ER retention. Co-expression of wt or mutant HA-tagged subunits, with β3 and γ2 subunits in HEK293T cells was carried out to assess assembly and trafficking to cell membranes. Reduced surface levels as well as total (whole cell lysate) levels were shown for α5(V294F). Surface levels and total levels of the α5(S413F) were not changed compared to wt. Surface levels of the β3 subunit were however lower in the case of α5(S413F), a finding which could be suggestive of a dominant negative effect. Both GABRA5 mutations resulted in decreased GABA-evoked current amplitudes in both neuronal and non-neuronal (HEK293T) cells.
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The corresponding phenotype in OMIM is Epileptic encephalopathy, early infantile, 79 (618559).
GABRA5 is not associated with any phenotype in G2P.

This gene is included in gene panels for ID offered by some diagnostic laboratories (eg. GeneDx).
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As a result, GABRA5 can be considered for inclusion in the ID and epilepsy panels probably as green (relevant phenotype, 3 unrelated individuals, 3 variants, supporting functional studies for all variants) or amber.
Created: 8 Sep 2019, 1:34 p.m. | Last Modified: 8 Sep 2019, 1:34 p.m.
Panel Version: 2.1022

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

Phenotypes
Epileptic encephalopathy, early infantile, 79 (MIM 618559)

Publications

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

Details

Mode of Inheritance
MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Sources
Phenotypes
  • Epileptic encephalopathy, early infantile, 79, 618559
  • developmental delay
OMIM
137142
Clinvar variants
Variants in GABRA5
Penetrance
None
Publications
Panels with this gene

History Filter Activity

30 Sep 2019, Gel status: 3

Entity classified by Genomics England curator

Rebecca Foulger (Genomics England curator)

Gene: gabra5 has been classified as Green List (High Evidence).

20 Sep 2019, Gel status: 2

Entity classified by Genomics England curator

Rebecca Foulger (Genomics England curator)

Gene: gabra5 has been classified as Amber List (Moderate Evidence).

20 Sep 2019, Gel status: 1

Set mode of inheritance

Rebecca Foulger (Genomics England curator)

Mode of inheritance for gene: GABRA5 was changed from to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown

20 Sep 2019, Gel status: 1

Set Phenotypes

Rebecca Foulger (Genomics England curator)

Phenotypes for gene: GABRA5 were changed from to Epileptic encephalopathy, early infantile, 79, 618559; developmental delay

20 Sep 2019, Gel status: 1

Set publications

Rebecca Foulger (Genomics England curator)

Publications for gene: GABRA5 were set to

28 Sep 2018, Gel status: 1

Created, Added New Source, Set mode of inheritance

Louise Daugherty (Genomics England Curator)

gene: GABRA5 was added gene: GABRA5 was added to Intellectual disability. Sources: Victorian Clinical Genetics Services Mode of inheritance for gene: GABRA5 was set to