GLRA3

glycine receptor alpha 3, the group of Glycine receptors

Basic information

Region (hg38): 4:174636919-174829247

Links

ENSG00000145451 ∙ NCBI:8001 ∙ OMIM:600421 ∙ HGNC:4328 ∙ Uniprot:O75311 ∙ 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 GLRA3 gene.

• Inborn genetic diseases (10 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GLRA3 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			10			10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	10	0	1

Variants in GLRA3

This is a list of pathogenic ClinVar variants found in the GLRA3 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-174643814-T-C		not specified	Uncertain significance (Dec 21, 2022)
4-174643892-G-A		not specified	Uncertain significance (Jun 22, 2021)
4-174643931-A-T		not specified	Uncertain significance (May 09, 2022)
4-174643970-T-C		not specified	Uncertain significance (Aug 12, 2021)
4-174644021-C-T		not specified	Uncertain significance (Jun 16, 2023)
4-174677155-C-A		not specified	Uncertain significance (Jan 03, 2024)
4-174677254-G-C		not specified	Uncertain significance (Mar 29, 2022)
4-174677277-A-G		not specified	Uncertain significance (Mar 01, 2024)
4-174682882-A-G		not specified	Uncertain significance (Sep 20, 2023)
4-174682923-A-T		not specified	Uncertain significance (Mar 13, 2023)
4-174766986-C-T		not specified	Uncertain significance (Feb 14, 2023)
4-174788905-C-T		not specified	Uncertain significance (Dec 18, 2023)
4-174788910-T-A		not specified	Uncertain significance (Jun 21, 2021)
4-174788932-G-A		not specified	Uncertain significance (Sep 22, 2021)
4-174828785-T-A			Benign (Nov 13, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GLRA3	protein_coding	protein_coding	ENST00000274093	10	192401

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000178	0.999	125718	0	30	125748	0.000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.985	212	256	0.827	0.0000131	3063
Missense in Polyphen		57	95.503	0.59684		1191
Synonymous	-0.462	96	90.4	1.06	0.00000477	851
Loss of Function	2.83	13	29.6	0.439	0.00000202	298

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000241	0.000241
Ashkenazi Jewish	0.000199	0.000198
East Asian	0.0000544	0.0000544
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000115	0.000114
Middle Eastern	0.0000544	0.0000544
South Asian	0.000163	0.000163
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Glycine receptors are ligand-gated chloride channels. Channel opening is triggered by extracellular glycine (PubMed:9677400, PubMed:26416729). Channel characteristics depend on the subunit composition; heteropentameric channels display faster channel closure (By similarity). Plays an important role in the down-regulation of neuronal excitability (By similarity). Contributes to the generation of inhibitory postsynaptic currents (By similarity). Contributes to increased pain perception in response to increased prostaglandin E2 levels (By similarity). Plays a role in cellular responses to ethanol (By similarity). {ECO:0000250|UniProtKB:P24524, ECO:0000250|UniProtKB:Q91XP5, ECO:0000269|PubMed:26416729, ECO:0000269|PubMed:9677400}.
• Pathway: Neuroactive ligand-receptor interaction - Homo sapiens (human);Neuronal System;Neurotransmitter receptors and postsynaptic signal transmission;Transmission across Chemical Synapses (Consensus)

Recessive Scores

• pRec: 0.163

Intolerance Scores

• loftool: 0.309
• rvis_EVS: -0.67
• rvis_percentile_EVS: 15.76

Haploinsufficiency Scores

• pHI: 0.460
• hipred: Y
• hipred_score: 0.544
• ghis: 0.577

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.501

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Glra3
• 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); 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)

Zebrafish Information Network

• Gene name: glra3
• Affected structure: mechanosensory behavior
• Phenotype tag: abnormal
• Phenotype quality: process quality

Gene ontology

• Biological process: signal transduction;neuropeptide signaling pathway;chemical synaptic transmission;ion transmembrane transport;regulation of membrane potential;response to amino acid;nervous system process;protein homooligomerization;synaptic transmission, glycinergic;excitatory postsynaptic potential;chloride transmembrane transport
• Cellular component: plasma membrane;integral component of plasma membrane;glycine-gated chloride channel complex;cell junction;dendrite;neuron projection;perikaryon;synapse;postsynaptic membrane
• Molecular function: transmembrane signaling receptor activity;extracellular ligand-gated ion channel activity;chloride channel activity;glycine binding;extracellularly glycine-gated chloride channel activity;glycine-gated chloride ion channel activity;metal ion binding