GABRA6

gamma-aminobutyric acid type A receptor subunit alpha6, the group of Gamma-aminobutyric acid type A receptor subunits

Basic information

Region (hg38): 5:161547062-161702593

Links

ENSG00000145863 ∙ NCBI:2559 ∙ OMIM:137143 ∙ HGNC:4080 ∙ Uniprot:Q16445 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the GABRA6 gene.

• Childhood absence epilepsy (21 variants)
• Inborn genetic diseases (12 variants)
• not provided (9 variants)
• Seizure (2 variants)
• GABRA6-Related Disorder (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GABRA6 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				8	7	15
missense			16	5	3	24
nonsense						0
start loss						0
frameshift			2			2
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding					2	2
Total	0	0	18	13	12

Variants in GABRA6

This is a list of pathogenic ClinVar variants found in the GABRA6 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
5-161548046-A-C		not specified	Likely benign (Dec 19, 2016)
5-161548050-G-T			Likely benign (Mar 30, 2018)
5-161548056-C-T		not specified	Likely benign (Jul 22, 2016)
5-161548062-C-T		not specified	Likely benign (Feb 21, 2017)
5-161548071-T-C		not specified	Likely benign (Sep 01, 2016)
5-161685994-C-T		not specified	Likely benign (Dec 14, 2022)
5-161685998-G-A		Childhood absence epilepsy • GABRA6-related disorder	Benign (Oct 13, 2023)
5-161686004-G-T			Likely benign (Aug 21, 2018)
5-161686251-A-G		Childhood absence epilepsy • GABRA6-related disorder	Benign/Likely benign (Feb 05, 2020)
5-161686285-G-A		not specified	Likely benign (Dec 11, 2023)
5-161686308-G-A			Likely benign (Jul 11, 2017)
5-161686334-G-A			Uncertain significance (May 09, 2021)
5-161686945-C-G		Seizure	Uncertain significance (May 01, 2020)
5-161688942-C-G			Likely benign (May 16, 2018)
5-161688978-G-C		Childhood absence epilepsy	Uncertain significance (Aug 28, 2021)
5-161688999-G-A			Likely benign (Oct 23, 2018)
5-161689062-G-A		Childhood absence epilepsy	Likely benign (Feb 27, 2017)
5-161689094-C-G		Childhood absence epilepsy	Uncertain significance (Mar 14, 2017)
5-161689314-T-C		Childhood absence epilepsy	Likely benign (Mar 05, 2021)
5-161689666-C-T		Childhood absence epilepsy	Benign (Aug 16, 2022)
5-161689667-G-T		GABRA6-related disorder	Likely benign (Nov 04, 2019)
5-161689680-C-A		not specified	Uncertain significance (Sep 06, 2023)
5-161689686-T-A		not specified	Uncertain significance (Feb 02, 2022)
5-161689700-C-A		Childhood absence epilepsy	Benign (Jul 03, 2023)
5-161689704-G-C		not specified	Uncertain significance (Aug 08, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GABRA6	protein_coding	protein_coding	ENST00000274545	9	155531

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.34e-12	0.0500	125686	0	62	125748	0.000247

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.409	257	239	1.07	0.0000128	2969
Missense in Polyphen		166	151.77	1.0938		1892
Synonymous	-1.47	107	89.3	1.20	0.00000541	882
Loss of Function	0.253	19	20.2	0.939	9.40e-7	254

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000748	0.000745
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000163	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.000273	0.000273
Middle Eastern	0.000163	0.000163
South Asian	0.000196	0.000196
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: GABA, the major inhibitory neurotransmitter in the vertebrate brain, mediates neuronal inhibition by binding to the GABA/benzodiazepine receptor and opening an integral chloride channel.
• Pathway: Retrograde endocannabinoid signaling - Homo sapiens (human);GABAergic synapse - Homo sapiens (human);Nicotine addiction - Homo sapiens (human);Neuroactive ligand-receptor interaction - Homo sapiens (human);Taste transduction - Homo sapiens (human);Morphine addiction - Homo sapiens (human);cardiac protection against ros;gamma-aminobutyric acid receptor life cycle pathway;GABA A receptor activation;Neuronal System;GABA receptor activation;Neurotransmitter receptors and postsynaptic signal transmission;Transmission across Chemical Synapses (Consensus)

Recessive Scores

• pRec: 0.160

Intolerance Scores

• loftool: 0.505
• rvis_EVS: 0.22
• rvis_percentile_EVS: 68.44

Haploinsufficiency Scores

• pHI: 0.791
• hipred: N
• hipred_score: 0.449

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.203

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Gabra6
• Phenotype: normal phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); hearing/vestibular/ear phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: signal transduction;gamma-aminobutyric acid signaling pathway;chemical synaptic transmission;ion transmembrane transport;regulation of membrane potential;nervous system process;synaptic transmission, GABAergic;regulation of postsynaptic membrane potential;chloride transmembrane transport
• Cellular component: plasma membrane;integral component of plasma membrane;cell junction;dendrite membrane;chloride channel complex;neuron projection;synapse;postsynaptic membrane;postsynapse;cerebellar Golgi cell to granule cell synapse;GABA-A receptor complex
• Molecular function: GABA-A receptor activity;extracellular ligand-gated ion channel activity;inhibitory extracellular ligand-gated ion channel activity;chloride channel activity;benzodiazepine receptor activity;GABA-gated chloride ion channel activity;transmitter-gated ion channel activity involved in regulation of postsynaptic membrane potential