GABRR2

gamma-aminobutyric acid type A receptor subunit rho2, the group of Gamma-aminobutyric acid type A receptor subunits

Basic information

Region (hg38): 6:89254463-89315299

Links

ENSG00000111886 ∙ NCBI:2570 ∙ OMIM:137162 ∙ HGNC:4091 ∙ Uniprot:P28476 ∙ 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 GABRR2 gene.

• Inborn genetic diseases (26 variants)
• not provided (9 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GABRR2 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				2	2	4
missense			24	2	2	28
nonsense			1			1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			2			2
Total	0	0	27	4	4

Variants in GABRR2

This is a list of pathogenic ClinVar variants found in the GABRR2 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-89257682-T-A			Likely benign (Apr 25, 2018)
6-89257692-A-G		not specified	Uncertain significance (Jun 11, 2021)
6-89257749-G-A		not specified	Uncertain significance (Feb 27, 2023)
6-89257768-T-C		not specified	Uncertain significance (Oct 20, 2021)
6-89257770-C-T			Likely benign (May 01, 2023)
6-89257779-G-A			Benign (Sep 17, 2019)
6-89257815-T-C		not specified	Uncertain significance (May 17, 2023)
6-89257960-G-A		not specified	Uncertain significance (Aug 11, 2022)
6-89264443-T-C			Benign (Jul 17, 2018)
6-89264495-C-T		Progressive sensorineural hearing impairment	Uncertain significance (Sep 03, 2016)
6-89264500-A-C		not specified	Uncertain significance (Jul 05, 2023)
6-89264508-G-A			Benign (Jun 14, 2018)
6-89264546-C-T		not specified	Uncertain significance (Feb 15, 2023)
6-89264551-G-A		not specified	Uncertain significance (Sep 01, 2021)
6-89264584-G-A		not specified	Uncertain significance (Nov 10, 2022)
6-89265642-C-T		not specified	Likely benign (Dec 07, 2021)
6-89265643-G-A		not specified	Uncertain significance (Jun 29, 2023)
6-89265686-G-A			Likely benign (Apr 10, 2018)
6-89265735-G-A		not specified	Uncertain significance (Nov 08, 2022)
6-89265736-T-A		not specified	Uncertain significance (May 26, 2022)
6-89265745-T-C		not specified	Uncertain significance (Aug 17, 2022)
6-89267787-A-T		not specified	Uncertain significance (Sep 14, 2022)
6-89267816-G-A		not specified	Uncertain significance (Jul 27, 2022)
6-89268041-G-A			Uncertain significance (Jan 01, 2022)
6-89269053-A-G		not specified	Uncertain significance (Jan 23, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GABRR2	protein_coding	protein_coding	ENST00000402938	9	58092

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000146	0.964	125693	0	55	125748	0.000219

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.296	268	282	0.950	0.0000166	3082
Missense in Polyphen		132	142.95	0.92343		1578
Synonymous	0.250	111	114	0.970	0.00000742	878
Loss of Function	1.93	11	20.4	0.540	9.46e-7	247

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000422	0.000421
Ashkenazi Jewish	0.00165	0.00159
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000187	0.000176
Middle Eastern	0.0000544	0.0000544
South Asian	0.000262	0.000261
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-2 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);MECP2 and Associated Rett Syndrome;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: 0.130

Intolerance Scores

• rvis_EVS: 0.07
• rvis_percentile_EVS: 59.11

Haploinsufficiency Scores

• pHI: 0.137
• hipred: N
• hipred_score: 0.350
• ghis: 0.469

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.141

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gabrr2
• Phenotype: endocrine/exocrine gland phenotype; reproductive system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan)

Gene ontology

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