GABRP

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

Basic information

Region (hg38): 5:170763350-170814047

Links

ENSG00000094755 ∙ NCBI:2568 ∙ OMIM:602729 ∙ HGNC:4089 ∙ Uniprot:O00591 ∙ 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 GABRP gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GABRP 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						0
missense			24	4	1	29
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	25	4	1

Variants in GABRP

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

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

Position	Type	Phenotype	Significance	ClinVar
5-170789133-T-C		not specified	Uncertain significance (Feb 13, 2024)
5-170789140-A-G		not specified	Uncertain significance (May 11, 2022)
5-170789166-G-A		not specified	Likely benign (May 31, 2023)
5-170789190-C-A		not specified	Uncertain significance (Apr 04, 2023)
5-170789202-A-G		not specified	Uncertain significance (Jun 17, 2024)
5-170794255-C-G		not specified	Uncertain significance (Aug 02, 2021)
5-170795276-G-C		not specified	Uncertain significance (Mar 24, 2023)
5-170795353-T-C		not specified	Uncertain significance (Jan 22, 2024)
5-170795374-G-A		not specified	Uncertain significance (Nov 05, 2021)
5-170795388-C-T		not specified	Uncertain significance (Mar 28, 2024)
5-170795396-C-G		not specified	Uncertain significance (Feb 23, 2023)
5-170795407-C-T		not specified	Uncertain significance (Aug 17, 2021)
5-170795412-C-A		not specified	Uncertain significance (Dec 17, 2023)
5-170797489-A-G		not specified	Uncertain significance (Feb 16, 2023)
5-170797491-A-G		not specified	Uncertain significance (Oct 29, 2021)
5-170805773-G-A			Benign (May 21, 2018)
5-170805779-TG-T			Uncertain significance (Jul 08, 2015)
5-170805790-C-T		not specified	Uncertain significance (Jun 03, 2022)
5-170805791-G-A		not specified	Uncertain significance (Nov 08, 2022)
5-170805849-G-C		not specified	Uncertain significance (Oct 18, 2021)
5-170808636-G-A		not specified	Uncertain significance (Aug 17, 2021)
5-170808671-G-A		not specified	Uncertain significance (Mar 06, 2023)
5-170808696-T-C		not specified	Uncertain significance (Aug 02, 2023)
5-170811963-C-T			Likely benign (May 21, 2018)
5-170811975-A-G		not specified	Uncertain significance (May 18, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GABRP	protein_coding	protein_coding	ENST00000518525	9	50698

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.82e-13	0.0300	125693	0	55	125748	0.000219

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.164	242	249	0.971	0.0000141	2902
Missense in Polyphen		104	104.95	0.991		1232
Synonymous	-0.985	111	98.6	1.13	0.00000576	835
Loss of Function	0.137	20	20.7	0.967	0.00000106	244

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000676	0.000676
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.000109	0.000109
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000177	0.000176
Middle Eastern	0.000109	0.000109
South Asian	0.000332	0.000327
Other	0.000163	0.000163

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. In the uterus, the function of the receptor appears to be related to tissue contractility. The binding of this pI subunit with other GABA(A) receptor subunits alters the sensitivity of recombinant receptors to modulatory agents such as pregnanolone.
• 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: 0.170

Intolerance Scores

• loftool: 0.433
• rvis_EVS: 0.27
• rvis_percentile_EVS: 70.58

Haploinsufficiency Scores

• pHI: 0.125
• hipred: N
• hipred_score: 0.459
• ghis: 0.407

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.335

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gabrp
• Phenotype: normal phenotype

Gene ontology

• Biological process: signal transduction;chemical synaptic transmission;ion transmembrane transport;regulation of membrane potential;nervous system process;chloride transmembrane transport
• Cellular component: integral component of plasma membrane;cell junction;chloride channel complex;neuron projection;synapse;postsynaptic membrane;GABA-A receptor complex
• Molecular function: GABA-A receptor activity;extracellular ligand-gated ion channel activity;chloride channel activity