GABRG1

gamma-aminobutyric acid type A receptor subunit gamma1, the group of Gamma-aminobutyric acid type A receptor subunits

Basic information

Region (hg38): 4:46035768-46124054

Links

ENSG00000163285 ∙ NCBI:2565 ∙ OMIM:137166 ∙ HGNC:4086 ∙ Uniprot:Q8N1C3 ∙ 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 GABRG1 gene.

• Inborn genetic diseases (15 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GABRG1 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					1	1
missense			15			15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	15	0	1

Variants in GABRG1

This is a list of pathogenic ClinVar variants found in the GABRG1 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-46041008-C-T		not specified	Uncertain significance (Jul 25, 2023)
4-46041051-T-C		not specified	Uncertain significance (Oct 30, 2023)
4-46041121-C-G		not specified	Uncertain significance (Jan 23, 2024)
4-46041153-A-C		not specified	Uncertain significance (Jun 29, 2022)
4-46041161-C-A		not specified	Uncertain significance (Dec 01, 2022)
4-46041205-A-G		not specified	Uncertain significance (Jul 14, 2021)
4-46041215-T-C		not specified	Uncertain significance (Mar 24, 2023)
4-46041238-T-C		not specified	Uncertain significance (Jan 07, 2022)
4-46051425-G-A		not specified	Uncertain significance (Feb 27, 2023)
4-46051456-T-C		not specified	Uncertain significance (Dec 16, 2022)
4-46051482-G-A		not specified	Uncertain significance (Jan 10, 2023)
4-46058606-A-C		not specified	Uncertain significance (Jan 26, 2022)
4-46064477-T-C		not specified	Uncertain significance (Feb 27, 2023)
4-46065519-G-A			Benign (Jan 25, 2018)
4-46065534-T-G		not specified	Uncertain significance (Oct 04, 2022)
4-46065536-A-C		not specified	Uncertain significance (Dec 03, 2021)
4-46065565-A-T		not specified	Uncertain significance (Feb 17, 2023)
4-46065578-T-C		not specified	Uncertain significance (Feb 17, 2023)
4-46097206-A-G		not specified	Uncertain significance (May 04, 2023)
4-46097282-T-C		not specified	Uncertain significance (Oct 20, 2023)
4-46097325-A-T		not specified	Uncertain significance (Dec 17, 2023)
4-46123877-G-T		not specified	Uncertain significance (Dec 17, 2023)
4-46123882-G-A		Malignant tumor of prostate	Uncertain significance (-)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GABRG1	protein_coding	protein_coding	ENST00000295452	9	88313

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000976	0.988	125719	0	22	125741	0.0000875

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.519	220	243	0.906	0.0000120	3052
Missense in Polyphen		82	100.12	0.81898		1283
Synonymous	-1.46	100	83.1	1.20	0.00000407	867
Loss of Function	2.22	10	21.0	0.476	0.00000105	273

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000184	0.000183
Ashkenazi Jewish	0.00	0.00
East Asian	0.000273	0.000272
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.0000898	0.0000879
Middle Eastern	0.000273	0.000272
South Asian	0.0000654	0.0000653
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 (Consensus)

Recessive Scores

• pRec: 0.0896

Intolerance Scores

• loftool: 0.332
• rvis_EVS: -0.8
• rvis_percentile_EVS: 12.24

Haploinsufficiency Scores

• pHI: 0.0973
• hipred: N
• hipred_score: 0.368
• ghis: 0.582

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.177

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gabrg1

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: 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;GABA receptor binding;transmitter-gated ion channel activity involved in regulation of postsynaptic membrane potential