Human Gene Module / Chromosome 5 / GABRG2

GABRG2gamma-aminobutyric acid type A receptor subunit gamma 2

SFARI Gene Score
3
Suggestive Evidence Criteria 3.1
Autism Reports / Total Reports
7 / 11
Rare Variants / Common Variants
19 / 0
Aliases
-
Associated Syndromes
-
Chromosome Band
5q34
Associated Disorders
-
Relevance to Autism

Multiple de novo variants in the GABRG2 gene, including a de novo loss-of-function variant and several de novo missense variants that are predicted to be deleterious, have been identified in ASD probands (De Rubeis et al., 2014; Zhou et al., 2022; Miyake et al., 2023); two of the ASD-associated missense variants in this gene had previously been identified in individuals with developmental and epileptic encephalpathy in Shen et al., 2016 and experimentally shown to result in reduced surface expression and decreased GABA-evoked whole-cell current amplitudes. Additional loss-of-function and missense variants with CADD scores > 30 were reported in individuals with a primary diagnosis of ASD in Wang et al., 2020. Hand stereotypies were reported in 1 of 8 individuals with de novo GABRG2 missense variants resulting in developmental and epileptic encephalopathy in Shen et al., 2016, and autism spectrum disorder was diagnosed in a patient with a p.Pro83Ser missense variant that had previously been identified in a family with idiopathic generalized epilepsy in Komulainen-Ebrahim et al., 2019. A polymorphism in the GABRG2 gene had previously been shown to be overrepresented in ASD cases by haplotype analysis (Sesarini et al., 2015).

Molecular Function

This gene encodes a gamma-aminobutyric acid (GABA) receptor. GABA is the major inhibitory neurotransmitter in the mammlian brain, where it acts at GABA-A receptors, which are ligand-gated chloride channels. GABA-A receptors are pentameric, consisting of proteins from several subunit classes: alpha, beta, gamma, delta and rho. Mutations in this gene are responsible for developmental and epileptic encephalopathy-74 (DEE74; OMIM 618396) and familial febrile seizures-8 (FEB8; OMIM 607681).

SFARI Genomic Platforms
Reports related to GABRG2 (11 Reports)
# Type Title Author, Year Autism Report Associated Disorders
1 Negative Association Identification of significant association and gene-gene interaction of GABA receptor subunit genes in autism Ma DQ , et al. (2005) Yes -
2 Negative Association - Sesarini CV et al. (2014) Yes -
3 Support Synaptic, transcriptional and chromatin genes disrupted in autism De Rubeis S , et al. (2014) Yes -
4 Positive Association - Sesarini CV et al. (2015) Yes -
5 Support - Shen D et al. (2017) No Stereotypy
6 Support - Komulainen-Ebrahim J et al. (2019) No ASD, stereotypy
7 Support Large-scale targeted sequencing identifies risk genes for neurodevelopmental disorders Wang T et al. (2020) Yes ID
8 Support - Zhou X et al. (2022) Yes -
9 Primary - Miyake N et al. (2023) Yes -
10 Support - Jiahui Sui et al. (2024) No -
11 Support - Purvi Majethia et al. (2024) No -
Rare Variants   (19)
Status Allele Change Residue Change Variant Type Inheritance Pattern Parental Transmission Family Type PubMed ID Author, Year
c.44C>A p.Ser15Ter stop_gained Unknown - - 33004838 Wang T et al. (2020)
c.889G>A p.Gly297Arg missense_variant Unknown - - 33004838 Wang T et al. (2020)
c.1094C>T p.Ser365Leu missense_variant Unknown - - 33004838 Wang T et al. (2020)
c.1291C>T p.Arg431Cys missense_variant Unknown - - 33004838 Wang T et al. (2020)
c.1375G>T p.Val459Phe missense_variant De novo - - 35982159 Zhou X et al. (2022)
c.968G>A p.Arg323Gln missense_variant De novo - - 25363760 De Rubeis S , et al. (2014)
c.316G>A p.Ala106Thr missense_variant De novo - Simplex 27864268 Shen D et al. (2017)
c.320T>C p.Ile107Thr missense_variant De novo - Simplex 27864268 Shen D et al. (2017)
c.844C>T p.Pro282Ser missense_variant De novo - Simplex 27864268 Shen D et al. (2017)
c.967C>T p.Arg323Trp missense_variant De novo - Simplex 27864268 Shen D et al. (2017)
c.968G>A p.Cys323Tyr missense_variant De novo - Simplex 27864268 Shen D et al. (2017)
c.1027T>C p.Phe343Leu missense_variant De novo - Simplex 27864268 Shen D et al. (2017)
c.853C>G p.Leu285Val missense_variant De novo - - 38374498 Purvi Majethia et al. (2024)
c.316G>A p.Ala106Thr missense_variant De novo - Simplex 36973392 Miyake N et al. (2023)
c.1374del p.Asp458GlufsTer85 frameshift_variant De novo - - 35982159 Zhou X et al. (2022)
c.42_43delinsAA p.Tyr14_Ser15delinsTer stop_gained Unknown - - 33004838 Wang T et al. (2020)
c.844C>A p.Pro282Thr missense_variant De novo - Simplex 31004928 Komulainen-Ebrahim J et al. (2019)
c.917C>T p.Ser306Phe missense_variant De novo - Simplex 31004928 Komulainen-Ebrahim J et al. (2019)
c.247C>T p.Pro83Ser missense_variant Familial Paternal Multiplex 31004928 Komulainen-Ebrahim J et al. (2019)
Common Variants  

No common variants reported.

SFARI Gene score
3

Suggestive Evidence

Score Delta: Score remained at 3

3

Suggestive Evidence

See all Category 3 Genes

The literature is replete with relatively small studies of candidate genes, using either common or rare variant approaches, which do not reach the criteria set out for categories 1 and 2. Genes that had two such lines of supporting evidence were placed in category 3, and those with one line of evidence were placed in category 4. Some additional lines of "accessory evidence" (indicated as "acc" in the score cards) could also boost a gene from category 4 to 3.

7/1/2023
icon
3

Increased from to 3

Krishnan Probability Score

Score 0.59279846587765

Ranking 464/25841 scored genes


[Show Scoring Methodology]
Krishnan and colleagues generated probability scores genome-wide by using a machine learning approach on a human brain-specific gene network. The method was first presented in Nat Neurosci 19, 1454-1462 (2016), and scores for more than 25,000 RefSeq genes can be accessed in column G of supplementary table 3 (see: http://www.nature.com/neuro/journal/v19/n11/extref/nn.4353-S5.xlsx). A searchable browser, with the ability to view networks of associated ASD risk genes, can be found at asd.princeton.edu.
ExAC Score

Score 0.95854339815542

Ranking 2557/18225 scored genes


[Show Scoring Methodology]
The Exome Aggregation Consortium (ExAC) is a summary database of 60,706 exomes that has been widely used to estimate 'constraint' on mutation for individual genes. It was introduced by Lek et al. Nature 536, 285-291 (2016), and the ExAC browser can be found at exac.broadinstitute.org. The pLI score was developed as measure of intolerance to loss-of- function mutation. A pLI > 0.9 is generally viewed as highly constrained, and thus any loss-of- function mutations in autism in such a gene would be more likely to confer risk. For a full list of pLI scores see: ftp://ftp.broadinstitute.org/pub/ExAC_release/release0.3.1/functional_gene_constraint/fordist_cle aned_exac_nonTCGA_z_pli_rec_null_data.txt
Sanders TADA Score

Score 0.71107613427568

Ranking 1230/18665 scored genes


[Show Scoring Methodology]
The TADA score ('Transmission and De novo Association') was introduced by He et al. PLoS Genet 9(8):e1003671 (2013), and is a statistic that integrates evidence from both de novo and transmitted mutations. It forms the basis for the claim of 65 individual genes being strongly associated with autism risk at a false discovery rate of 0.1 (Sanders et al. Neuron 87, 1215-1233 (2015)). The calculated TADA score for 18,665 RefSeq genes can be found in column P of Supplementary Table 6 in the Sanders et al. paper (the column headed 'tadaFdrAscSscExomeSscAgpSmallDel'), which represents a combined analysis of exome data and small de novo deletions (see www.cell.com/cms/attachment/2038545319/2052606711/mmc7.xlsx).
Zhang D Score

Score 0.23903287598109

Ranking 3634/20870 scored genes


[Show Scoring Methodology]
The DAMAGES score (disease-associated mutation analysis using gene expression signatures), or D score, was developed to combine evidence from de novo loss-of- function mutation with evidence from cell-type- specific gene expression in the mouse brain (specifically translational profiles of 24 specific mouse CNS cell types isolated from 6 different brain regions). Genes with positive D scores are more likely to be associated with autism risk, with higher-confidence genes having higher D scores. This statistic was first presented by Zhang & Shen (Hum Mutat 38, 204- 215 (2017), and D scores for more than 20,000 RefSeq genes can be found in column M in supplementary table 2 from that paper.
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