GABRE

gamma-aminobutyric acid type A receptor subunit epsilon, the group of Gamma-aminobutyric acid type A receptor subunits|MicroRNA protein coding host genes

Basic information

Region (hg38): X:151953123-151974680

Links

ENSG00000102287 ∙ NCBI:2564 ∙ OMIM:300093 ∙ HGNC:4085 ∙ Uniprot:P78334 ∙ 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 GABRE gene.

• Inborn genetic diseases (17 variants)
• not provided (14 variants)
• GABRE-related epilepsy (1 variants)
• GABRE-related condition (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GABRE 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				3	2	5
missense			21	1	3	25
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				3		3
non coding						0
Total	0	0	21	4	5

Variants in GABRE

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

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

Position	Type	Phenotype	Significance	ClinVar
X-151954786-C-A		not specified	Uncertain significance (Mar 07, 2023)
X-151954807-C-T		GABRE-related disorder	Likely benign (Nov 26, 2021)
X-151954868-G-C			Benign (Apr 03, 2018)
X-151954875-C-G		not specified	Uncertain significance (Aug 19, 2023)
X-151954910-G-A		not specified	Uncertain significance (Jan 30, 2024)
X-151954917-C-G			Benign (May 09, 2018)
X-151955029-G-A		not specified	Uncertain significance (Mar 01, 2023)
X-151955033-A-G			Uncertain significance (Mar 03, 2021)
X-151955045-G-A		GABRE-related epilepsy	Uncertain significance (Jan 07, 2022)
X-151955045-G-C		not specified	Uncertain significance (Jan 30, 2024)
X-151955050-C-T		not specified	Uncertain significance (Jan 08, 2024)
X-151955051-G-A		not specified	Uncertain significance (Dec 16, 2023)
X-151955056-C-T		not specified	Uncertain significance (Jun 22, 2021)
X-151955060-C-T			Likely benign (-)
X-151955069-G-A		not specified	Uncertain significance (Dec 01, 2022)
X-151955373-G-A		not specified	Uncertain significance (Oct 03, 2022)
X-151955379-T-C		not specified	Uncertain significance (Feb 23, 2023)
X-151955445-C-T		not specified	Uncertain significance (Nov 23, 2022)
X-151955472-C-T		not specified	Uncertain significance (Oct 27, 2022)
X-151955509-C-T			Likely benign (Mar 01, 2020)
X-151955522-C-T		not specified	Uncertain significance (Feb 21, 2024)
X-151955530-G-T			Uncertain significance (-)
X-151955538-A-G			Benign (Sep 29, 2017)
X-151955540-G-A		not specified	Uncertain significance (Dec 03, 2021)
X-151955702-T-A			Likely benign (Feb 01, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GABRE	protein_coding	protein_coding	ENST00000370328	9	21557

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000184	0.903	125732	7	7	125746	0.0000557

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0720	211	208	1.01	0.0000172	3322
Missense in Polyphen		65	87.903	0.73945		1349
Synonymous	0.605	70	76.7	0.912	0.00000620	982
Loss of Function	1.51	8	14.1	0.567	9.55e-7	254

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000228	0.000185
Ashkenazi Jewish	0.00	0.00
East Asian	0.000144	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.000112	0.0000791
Middle Eastern	0.000144	0.000109
South Asian	0.00	0.00
Other	0.00	0.00

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);Morphine addiction - Homo sapiens (human);GABA receptor Signaling (Consensus)

Recessive Scores

• pRec: 0.135

Intolerance Scores

• loftool: 0.188
• rvis_EVS: 1.82
• rvis_percentile_EVS: 97.01

Haploinsufficiency Scores

• pHI: 0.416
• hipred: N
• hipred_score: 0.215
• ghis: 0.400

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.254

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gabre

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;negative regulation of chloride transport
• Cellular component: integral component of plasma membrane;cell junction;dendrite membrane;chloride channel complex;neuron projection;synapse;postsynaptic membrane;postsynapse;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