GABRG2
protein-codinggamma-aminobutyric acid type A receptor subunit gamma2, the group of Gamma-aminobutyric acid type A receptor subunits
Gene summary
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 have been associated with epilepsy and febrile seizures. Multiple transcript variants encoding different isoforms have been identified for this gene. [provided by RefSeq, Jul 2008]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~162.9 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AD
Disease ID:MONDO:0011891
Submitter: G2P
Inheritance Pattern: AD
Disease ID:MONDO:0011891
Submitter: PanelApp Australia
Inheritance Pattern: AD
Disease ID:MONDO:0032725
Submitter: PanelApp Australia
Inheritance Pattern: AD
Disease ID:MONDO:0011794
Submitter: Orphanet
Inheritance Pattern: AD
Disease ID:MONDO:0011891
Submitter: Ambry Genetics
Inheritance Pattern: AD
Disease ID:MONDO:0007295
Submitter: Orphanet
Inheritance Pattern: AD
Disease ID:MONDO:0011891
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AD
Disease ID:MONDO:0032725
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AD
Disease ID:MONDO:0018214
Submitter: Orphanet
Inheritance Pattern: AD
Disease ID:MONDO:0018614
Submitter: Orphanet
Inheritance Pattern: AD
Disease ID:MONDO:0005027
Submitter: ClinGen
GABRG2 was first reported in relation to autosomal dominant epilepsy as early as 2001 (Baulac et al., Wallace et al.; PMID: 11326274, 11326275). Eight unique variants (missense, nonsense, and splice site) are included in this curation to maximize the score for genetic evidence; however, more probands are available in the literature (PMID: 11326274, 12117362, 27066572, 27864268, 28460589, 31004928). Evidence supporting this gene-disease relationship includes case-level data, segregation data, and experimental data. Proband phenotypes included febrile seizures, complex partial seizures, childhood absence epilepsy, GEFS+, epileptic encephalopathy, epilepsy of infancy with migrating focal seizures, Lennox-like epilepsy, and Lennox-Gastaut syndrome. While these phenotypes exist on a spectrum, the Epilepsy GCEP decided to lump these conditions under the general term for epilepsy until more evidence is available. Variants in this gene segregated with disease in 16 additional family members across 3 families (PMID: 11326274, 12117362, 27066572). This gene-disease association is supported by multiple mouse models. In summary, GABRG2 is definitively associated with autosomal dominant epilepsy.
Clinical Genomic Database (CGD)
Manifestation: Neurologic
Intervention: General
Rationale: Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing; Many variants may involve a susceptibility locus and/or evidence or clinical applicability is unclear
Comments: As with other conditions involving seizures, optimal seizure control is beneficial, and awareness of genetic causes may help with medication selection
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to GABRG2 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_198904.4. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 6 | 126 | 132 | |||
| missense | 14 | 51 | 264 | 19 | 1 | 349 |
| nonsense | 15 | 14 | 3 | 32 | ||
| start loss | 3 | 3 | ||||
| frameshift | 26 | 10 | 4 | 40 | ||
| splice donor/acceptor (+/-2bp) | 4 | 14 | 7 | 25 | ||
| Total | 59 | 89 | 287 | 145 | 1 | 581 |
Highest pathogenic variant AF is 0.000008680383
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_944494.1 | 10 | MANE Select | |
| Ensembl | ENSP00000491909.2 | 10 | MANE Select | |
| RefSeq | NP_000807.2 | 9 | Standard | |
| RefSeq | NP_001362268.1 | 10 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Benzodiazepine Pathway, Pharmacodynamics
- Retrograde endocannabinoid signaling - Homo sapiens (human)
- GABAergic synapse - Homo sapiens (human)
- Nicotine addiction - Homo sapiens (human)
- Neuroactive ligand-receptor interaction - Homo sapiens (human)
Biological Process
- signal transduction
- gamma-aminobutyric acid signaling pathway
- chemical synaptic transmission
- post-embryonic development
- adult behavior
Molecular Function
- GABA-A receptor activity
- extracellular ligand-gated ion channel activity
- inhibitory extracellular ligand-gated ion channel activity
- chloride channel activity
- protein binding
Cellular Component
- plasma membrane
- integral component of plasma membrane
- cell junction
- axon
- cytoplasmic vesicle membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000414552
- Coding exons
- 11
- Length
- 87997
- Individuals with no LoFs
- 125711
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 5
- Defined
- 125716
- p
- 0.0000199
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 2.99 | 137 | 277 | 0.494 | 0.0000152 | 3377 |
| Missense (PolyPhen) | 53 | 154.45 | 0.34316 | 1942 | ||
| Synonymous | -0.794 | 108 | 98.0 | 1.10 | 0.00000506 | 970 |
| Loss of Function | 3.86 | 5 | 26.4 | 0.190 | 0.00000133 | 310 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0.000087 | 0.000058 | rare |
| Ashkenazi Jewish | 0.00010 | 0.000099 | rare |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.0000089 | 0.0000088 | rare |
| South Asian | 0.000033 | 0.000033 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Component of the heteropentameric receptor for GABA, the major inhibitory neurotransmitter in the vertebrate brain. Functions also as histamine receptor and mediates cellular responses to histamine. Functions as receptor for diazepines and various anesthetics, such as pentobarbital; these are bound at a separate allosteric effector binding site. Functions as ligand- gated chloride channel. {ECO:0000269|PubMed:2538761}.;
- Disease
- DISEASE: Epilepsy, childhood absence 2 (ECA2) [MIM:607681]: A subtype of idiopathic generalized epilepsy characterized by an onset at age 6-7 years, frequent absence seizures (several per day) and bilateral, synchronous, symmetric 3-Hz spike waves on EEG. Tonic-clonic seizures often develop in adolescence. Some individuals manifest febrile seizures. Absence seizures may either remit or persist into adulthood. {ECO:0000269|PubMed:11326275}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.; DISEASE: Febrile seizures, familial, 8 (FEB8) [MIM:611277]: Seizures associated with febrile episodes in childhood without any evidence of intracranial infection or defined pathologic or traumatic cause. It is a common condition, affecting 2-5% of children aged 3 months to 5 years. The majority are simple febrile seizures (generally defined as generalized onset, single seizures with a duration of less than 30 minutes). Complex febrile seizures are characterized by focal onset, duration greater than 30 minutes, and/or more than one seizure in a 24 hour period. The likelihood of developing epilepsy following simple febrile seizures is low. Complex febrile seizures are associated with a moderately increased incidence of epilepsy. {ECO:0000269|PubMed:16924025}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Generalized epilepsy with febrile seizures plus 3 (GEFS+3) [MIM:611277]: A rare autosomal dominant, familial condition with incomplete penetrance and large intrafamilial variability. Patients display febrile seizures persisting sometimes beyond the age of 6 years and/or a variety of afebrile seizure types. This disease combines febrile seizures, generalized seizures often precipitated by fever at age 6 years or more, and partial seizures, with a variable degree of severity. {ECO:0000269|PubMed:11326274, ECO:0000269|PubMed:23708187}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Recessive Scores
- pRec
- 0.208
Intolerance Scores
- LoFtool
- 0.0753
- RVIS EVS
- -0.43
- RVIS percentile EVS
- 25.15
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.780
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |