GABRR1

gamma-aminobutyric acid type A receptor subunit rho1, the group of Gamma-aminobutyric acid type A receptor subunits

Basic information

Region (hg38): 6:89177503-89231278

Links

ENSG00000146276 ∙ NCBI:2569 ∙ OMIM:137161 ∙ HGNC:4090 ∙ Uniprot:P24046 ∙ 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 GABRR1 gene.

• Inborn genetic diseases (18 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GABRR1 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			17	1		18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	17	1	1

Variants in GABRR1

This is a list of pathogenic ClinVar variants found in the GABRR1 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-89178825-A-G		not specified	Uncertain significance (Oct 10, 2023)
6-89178937-C-T		not specified	Uncertain significance (Jun 22, 2023)
6-89178943-T-A		not specified	Uncertain significance (Aug 20, 2023)
6-89179008-T-C		not specified	Uncertain significance (Feb 15, 2023)
6-89179026-G-A		not specified	Likely benign (Dec 01, 2022)
6-89180329-G-A		not specified	Uncertain significance (Jul 12, 2023)
6-89180345-C-T		not specified	Uncertain significance (Sep 22, 2023)
6-89180375-C-T		not specified	Uncertain significance (Dec 21, 2023)
6-89180386-C-T		not specified	Uncertain significance (Jan 30, 2024)
6-89180426-C-T		not specified	Uncertain significance (Dec 15, 2023)
6-89180429-G-A		not specified	Uncertain significance (May 11, 2022)
6-89180452-G-A		not specified	Uncertain significance (Jan 10, 2023)
6-89180458-A-G		not specified	Uncertain significance (Apr 17, 2023)
6-89181935-G-A		not specified	Uncertain significance (Apr 25, 2023)
6-89182022-G-A		not specified	Uncertain significance (Nov 18, 2022)
6-89182042-A-G		not specified	Uncertain significance (Dec 09, 2023)
6-89185381-C-T		not specified	Uncertain significance (Oct 05, 2022)
6-89185382-G-A		not specified	Uncertain significance (Mar 04, 2024)
6-89185409-C-A		not specified	Uncertain significance (Nov 09, 2023)
6-89190209-C-T		not specified	Uncertain significance (Aug 02, 2023)
6-89190231-T-C		not specified	Uncertain significance (Nov 13, 2023)
6-89198067-G-A			Benign (May 15, 2018)
6-89198098-C-T		not specified	Uncertain significance (Sep 22, 2022)
6-89198105-A-G		not specified	Uncertain significance (Aug 11, 2022)
6-89198141-T-G		not specified	Uncertain significance (Jan 08, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GABRR1	protein_coding	protein_coding	ENST00000454853	10	53778

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
8.65e-14	0.0707	125682	1	64	125747	0.000258

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.726	256	291	0.880	0.0000173	3191
Missense in Polyphen		104	146.82	0.70834		1645
Synonymous	-0.0438	112	111	1.01	0.00000733	885
Loss of Function	0.594	22	25.2	0.872	0.00000136	269

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000749	0.000747
Ashkenazi Jewish	0.00	0.00
East Asian	0.000652	0.000598
Finnish	0.00	0.00
European (Non-Finnish)	0.000230	0.000229
Middle Eastern	0.000652	0.000598
South Asian	0.000297	0.000294
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. Rho-1 GABA receptor could play a role in retinal neurotransmission.
• 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;Neuronal System;GABA A (rho) receptor activation;GABA receptor activation;Neurotransmitter receptors and postsynaptic signal transmission;Transmission across Chemical Synapses (Consensus)

Recessive Scores

• pRec: 0.121

Intolerance Scores

• loftool: 0.368
• rvis_EVS: 0.02
• rvis_percentile_EVS: 55.61

Haploinsufficiency Scores

• pHI: 0.164
• hipred: N
• hipred_score: 0.310
• ghis: 0.423

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.160

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gabrr1
• Phenotype: vision/eye phenotype; 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); taste/olfaction phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan)

Gene ontology

• Biological process: signal transduction;gamma-aminobutyric acid signaling pathway;chemical synaptic transmission;ion transmembrane transport;regulation of membrane potential;nervous system process;regulation of postsynaptic membrane potential;regulation of presynaptic membrane potential;chloride transmembrane transport
• Cellular component: plasma membrane;integral component of plasma membrane;cell junction;chloride channel complex;neuron projection;synapse;postsynaptic membrane;glutamatergic synapse;GABA-ergic synapse;GABA-A receptor complex
• Molecular function: GABA-A receptor activity;extracellular ligand-gated ion channel activity;chloride channel activity;ligand-gated ion channel activity involved in regulation of presynaptic membrane potential;transmitter-gated ion channel activity involved in regulation of postsynaptic membrane potential