GABRG2

protein-coding

gamma-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

NM_198904.4

Inheritance

AD

ClinVar variants

P:148U:287B:146

Top phenotype

Generalized epilepsy with febrile seizures plus, type 3; Familial febrile seizures 8; Developmental and epileptic encephalopathy 74

gnomAD constraint

pLI —, LoF o/e 0.19

Max pathogenic AF

—

Genomic locus

chr5:162,000,057-162,162,977

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~162.9 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

febrile seizures, familial, 8STRONG

Inheritance Pattern: AD

Disease ID:MONDO:0011891

Submitter: G2P

febrile seizures, familial, 8STRONG

Inheritance Pattern: AD

Disease ID:MONDO:0011891

Submitter: PanelApp Australia

developmental and epileptic encephalopathy, 74STRONG

Inheritance Pattern: AD

Disease ID:MONDO:0032725

Submitter: PanelApp Australia

Dravet syndromeSUPPORTIVE

Inheritance Pattern: AD

Disease ID:MONDO:0011794

Submitter: Orphanet

febrile seizures, familial, 8STRONG

Inheritance Pattern: AD

Disease ID:MONDO:0011891

Submitter: Ambry Genetics

self-limited epilepsy with centrotemporal spikesSUPPORTIVE

Inheritance Pattern: AD

Disease ID:MONDO:0007295

Submitter: Orphanet

febrile seizures, familial, 8STRONG

Inheritance Pattern: AD

Disease ID:MONDO:0011891

Submitter: Labcorp Genetics (formerly Invitae)

developmental and epileptic encephalopathy, 74STRONG

Inheritance Pattern: AD

Disease ID:MONDO:0032725

Submitter: Labcorp Genetics (formerly Invitae)

generalized epilepsy with febrile seizures plusSUPPORTIVE

Inheritance Pattern: AD

Disease ID:MONDO:0018214

Submitter: Orphanet

undetermined early-onset epileptic encephalopathySUPPORTIVE

Inheritance Pattern: AD

Disease ID:MONDO:0018614

Submitter: Orphanet

epilepsyDEFINITIVE

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)

Generalized epilepsy with febrile seizures plus, type 3; Familial febrile seizures 8; Developmental and epileptic encephalopathy 74AD

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

Refs: 11326274; 11326275; 1748509; 12117362; 17190949; 19261880; 20308251; 23069679; 27864268Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to GABRG2 variants in ClinVar

21 Conditions Cataloged
Febrile seizures, familial, 8Total: 543
EPILEPSY, CHILDHOOD ABSENCE, SUSCEPTIBILITY TO, 2Total: 530
not providedTotal: 230
not specifiedTotal: 81
Inborn genetic diseasesTotal: 71
GABRG2-related disorderTotal: 37
Developmental and epileptic encephalopathy, 74Total: 29
SeizureTotal: 8

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.

EffectPLPVUSLBBSum
synonymous
6
clinvar
126
clinvar
132
missense
14
clinvar
51
clinvar
264
clinvar
19
clinvar
1
clinvar
349
nonsense
15
clinvar
14
clinvar
3
clinvar
32
start loss
3
clinvar
3
frameshift
26
clinvar
10
clinvar
4
clinvar
40
splice donor/acceptor (+/-2bp)
4
clinvar
14
clinvar
7
clinvar
25
Total59892871451581

Highest pathogenic variant AF is 0.000008680383

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 50 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_198904.4RefSeqNP_944494.110MANE Select
ENST00000639213.2EnsemblENSP00000491909.210MANE Select
NM_000816.3RefSeqNP_000807.29Standard
NM_001375339.1RefSeqNP_001362268.110Standard

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: gnomAD

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-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense2.991372770.4940.00001523377
Missense (PolyPhen)53154.450.343161942
Synonymous-0.79410898.01.100.00000506970
Loss of Function3.86526.40.1900.00000133310

Population LoF Frequency

PopulationCAFp-valueStatus
African00.0absent
Latino/Admixed American0.0000870.000058rare
Ashkenazi Jewish0.000100.000099rare
East Asian00.0absent
Finnish00.0absent
European (Non-Finnish)0.00000890.0000088rare
South Asian0.0000330.000033rare
Other00.0absent

dbNSFP Gene Annotations

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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