GABRG3

gamma-aminobutyric acid type A receptor subunit gamma3, the group of Gamma-aminobutyric acid type A receptor subunits

Basic information

Region (hg38): 15:26971180-27541984

Links

ENSG00000182256 ∙ NCBI:2567 ∙ OMIM:600233 ∙ HGNC:4088 ∙ Uniprot:Q99928 ∙ 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 GABRG3 gene.

• Inborn genetic diseases (8 variants)
• not provided (6 variants)
• Angelman syndrome (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GABRG3 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	3
missense			8	1		9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)			1			1
splice region	1				1	2
non coding						0
Total	0	0	9	1	3

Variants in GABRG3

This is a list of pathogenic ClinVar variants found in the GABRG3 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-26977006-A-G		not specified	Uncertain significance (Mar 21, 2023)
15-26977087-G-A			Likely benign (Jun 23, 2018)
15-26977119-A-G			Benign (Dec 31, 2019)
15-27026765-G-A		not specified	Uncertain significance (Feb 06, 2024)
15-27026799-G-C		not specified	Uncertain significance (Mar 13, 2023)
15-27026829-G-A			Benign (Dec 31, 2019)
15-27326874-A-G			Uncertain significance (-)
15-27326938-C-T		not specified	Uncertain significance (Apr 25, 2022)
15-27327030-G-A			Uncertain significance (Feb 01, 2023)
15-27480668-A-C		not specified	Uncertain significance (May 16, 2022)
15-27480769-A-G		not specified	Uncertain significance (Dec 21, 2023)
15-27480771-C-T			Benign (Dec 31, 2019)
15-27480772-G-A		GABRG3-related disorder	Likely benign (Nov 11, 2022)
15-27520007-A-G		not specified	Uncertain significance (Mar 24, 2023)
15-27520009-T-C			Benign (Dec 31, 2019)
15-27527489-C-G		not specified	Uncertain significance (Sep 23, 2023)
15-27527589-C-G		not specified	Uncertain significance (Dec 09, 2023)
15-27527592-G-T		not specified	Uncertain significance (Feb 02, 2024)
15-27527607-C-G		not specified	Uncertain significance (Dec 12, 2023)
15-27527963-C-T		GABRG3-related disorder	Likely benign (Mar 16, 2022)
15-27532602-C-T		Angelman syndrome	Pathogenic (Mar 08, 2020)
15-27532628-C-G		not specified	Uncertain significance (Nov 10, 2022)
15-27532639-A-G		not specified	Uncertain significance (Jul 06, 2021)
15-27532697-A-T		not specified	Uncertain significance (Aug 12, 2021)
15-27532774-C-T		not specified	Uncertain significance (Aug 12, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GABRG3	protein_coding	protein_coding	ENST00000333743	10	561945

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.847	0.153	124641	0	9	124650	0.0000361

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.52	145	259	0.560	0.0000147	3021
Missense in Polyphen		62	136.63	0.45376		1538
Synonymous	-0.175	106	104	1.02	0.00000653	871
Loss of Function	3.76	4	23.8	0.168	0.00000116	297

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.0000994	0.0000993
East Asian	0.000113	0.000111
Finnish	0.00	0.00
European (Non-Finnish)	0.0000514	0.0000442
Middle Eastern	0.000113	0.000111
South Asian	0.0000374	0.0000327
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);Prader-Willi and Angelman Syndrome;GABA receptor Signaling;GABA A receptor activation;Neuronal System;GABA receptor activation;Neurotransmitter receptors and postsynaptic signal transmission;Transmission across Chemical Synapses (Consensus)

Recessive Scores

• pRec: 0.102

Intolerance Scores

• loftool: 0.196
• rvis_EVS: -0.09
• rvis_percentile_EVS: 46.74

Haploinsufficiency Scores

• pHI: 0.0885
• hipred: Y
• hipred_score: 0.809

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.205

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gabrg3

Gene ontology

• Biological process: signal transduction;gamma-aminobutyric acid signaling pathway;chemical synaptic transmission;ion transmembrane transport;regulation of membrane potential;response to drug;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;GABA-ergic synapse;integral component of synaptic membrane;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